Name: rs5863996
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs5863996

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:169413172-169413185 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: del(T)₄ / delTTT / delTT / delT / …
del(T)₄ / delTTT / delTT / delT / dupT / dupTT / dupTTT / dup(T)₈ / dup(T)₁₄
Variation Type: Indel Insertion and Deletion
Frequency: (T)₁₄=0.1997 (1000/5008, 1000G)
(T)₁₄=0.2130 (1029/4832, ALFA)
(T)₁₄=0.0867 (334/3854, ALSPAC) (+ 4 more)
(T)₁₄=0.0928 (344/3708, TWINSUK)
(T)₁₄=0.120 (120/998, GoNL)
(T)₁₄=0.137 (82/598, NorthernSweden)
(T)₁₄=0.10 (4/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NEK1 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	4832	TTTTTTTTTTTTTT=0.2130	TTTTTTTTTT=0.0000, TTTTTTTTTTTT=0.0002, TTTTTTTTTTTTT=0.7868, TTTTTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTTTT=0.0000	0.09441	0.668323	0.237267	32
European	Sub	4546	TTTTTTTTTTTTTT=0.1648	TTTTTTTTTT=0.0000, TTTTTTTTTTTT=0.0002, TTTTTTTTTTTTT=0.8350, TTTTTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTTTT=0.0000	0.038732	0.709067	0.252201	9
African	Sub	256	TTTTTTTTTTTTTT=1.000	TTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
African Others	Sub	10	TTTTTTTTTTTTTT=1.0	TTTTTTTTTT=0.0, TTTTTTTTTTTT=0.0, TTTTTTTTTTTTT=0.0, TTTTTTTTTTTTTTT=0.0, TTTTTTTTTTTTTTTT=0.0	1.0	0.0	0.0	N/A
African American	Sub	246	TTTTTTTTTTTTTT=1.000	TTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
Asian	Sub	0	TTTTTTTTTTTTTT=0	TTTTTTTTTT=0, TTTTTTTTTTTT=0, TTTTTTTTTTTTT=0, TTTTTTTTTTTTTTT=0, TTTTTTTTTTTTTTTT=0	0	0	0	N/A
East Asian	Sub	0	TTTTTTTTTTTTTT=0	TTTTTTTTTT=0, TTTTTTTTTTTT=0, TTTTTTTTTTTTT=0, TTTTTTTTTTTTTTT=0, TTTTTTTTTTTTTTTT=0	0	0	0	N/A
Other Asian	Sub	0	TTTTTTTTTTTTTT=0	TTTTTTTTTT=0, TTTTTTTTTTTT=0, TTTTTTTTTTTTT=0, TTTTTTTTTTTTTTT=0, TTTTTTTTTTTTTTTT=0	0	0	0	N/A
Latin American 1	Sub	4	TTTTTTTTTTTTTT=1.0	TTTTTTTTTT=0.0, TTTTTTTTTTTT=0.0, TTTTTTTTTTTTT=0.0, TTTTTTTTTTTTTTT=0.0, TTTTTTTTTTTTTTTT=0.0	1.0	0.0	0.0	N/A
Latin American 2	Sub	10	TTTTTTTTTTTTTT=1.0	TTTTTTTTTT=0.0, TTTTTTTTTTTT=0.0, TTTTTTTTTTTTT=0.0, TTTTTTTTTTTTTTT=0.0, TTTTTTTTTTTTTTTT=0.0	1.0	0.0	0.0	N/A
South Asian	Sub	0	TTTTTTTTTTTTTT=0	TTTTTTTTTT=0, TTTTTTTTTTTT=0, TTTTTTTTTTTTT=0, TTTTTTTTTTTTTTT=0, TTTTTTTTTTTTTTTT=0	0	0	0	N/A
Other	Sub	16	TTTTTTTTTTTTTT=0.62	TTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.38, TTTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTTT=0.00	0.625	0.375	0.0	5

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
1000Genomes	Global	Study-wide	5008	(T)₁₄=0.1997	delT=0.8003
1000Genomes	African	Sub	1322	(T)₁₄=0.3691	delT=0.6309
1000Genomes	East Asian	Sub	1008	(T)₁₄=0.1915	delT=0.8085
1000Genomes	Europe	Sub	1006	(T)₁₄=0.1213	delT=0.8787
1000Genomes	South Asian	Sub	978	(T)₁₄=0.106	delT=0.894
1000Genomes	American	Sub	694	(T)₁₄=0.134	delT=0.866
Allele Frequency Aggregator	Total	Global	4832	(T)₁₄=0.2130	del(T)₄=0.0000, delTT=0.0002, delT=0.7868, dupT=0.0000, dupTT=0.0000
Allele Frequency Aggregator	European	Sub	4546	(T)₁₄=0.1648	del(T)₄=0.0000, delTT=0.0002, delT=0.8350, dupT=0.0000, dupTT=0.0000
Allele Frequency Aggregator	African	Sub	256	(T)₁₄=1.000	del(T)₄=0.000, delTT=0.000, delT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	Other	Sub	16	(T)₁₄=0.62	del(T)₄=0.00, delTT=0.00, delT=0.38, dupT=0.00, dupTT=0.00
Allele Frequency Aggregator	Latin American 2	Sub	10	(T)₁₄=1.0	del(T)₄=0.0, delTT=0.0, delT=0.0, dupT=0.0, dupTT=0.0
Allele Frequency Aggregator	Latin American 1	Sub	4	(T)₁₄=1.0	del(T)₄=0.0, delTT=0.0, delT=0.0, dupT=0.0, dupTT=0.0
Allele Frequency Aggregator	South Asian	Sub	0	(T)₁₄=0	del(T)₄=0, delTT=0, delT=0, dupT=0, dupTT=0
Allele Frequency Aggregator	Asian	Sub	0	(T)₁₄=0	del(T)₄=0, delTT=0, delT=0, dupT=0, dupTT=0
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	(T)₁₄=0.0867	delT=0.9133
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	(T)₁₄=0.0928	delT=0.9072
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	(T)₁₄=0.120	delT=0.880
Northern Sweden	ACPOP	Study-wide	598	(T)₁₄=0.137	delT=0.863
The Danish reference pan genome	Danish	Study-wide	40	(T)₁₄=0.10	delT=0.90

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 4	NC_000004.12:g.169413182_169413185del
GRCh38.p14 chr 4	NC_000004.12:g.169413183_169413185del
GRCh38.p14 chr 4	NC_000004.12:g.169413184_169413185del
GRCh38.p14 chr 4	NC_000004.12:g.169413185del
GRCh38.p14 chr 4	NC_000004.12:g.169413185dup
GRCh38.p14 chr 4	NC_000004.12:g.169413184_169413185dup
GRCh38.p14 chr 4	NC_000004.12:g.169413183_169413185dup
GRCh38.p14 chr 4	NC_000004.12:g.169413178_169413185dup
GRCh38.p14 chr 4	NC_000004.12:g.169413172_169413185dup
GRCh37.p13 chr 4	NC_000004.11:g.170334333_170334336del
GRCh37.p13 chr 4	NC_000004.11:g.170334334_170334336del
GRCh37.p13 chr 4	NC_000004.11:g.170334335_170334336del
GRCh37.p13 chr 4	NC_000004.11:g.170334336del
GRCh37.p13 chr 4	NC_000004.11:g.170334336dup
GRCh37.p13 chr 4	NC_000004.11:g.170334335_170334336dup
GRCh37.p13 chr 4	NC_000004.11:g.170334334_170334336dup
GRCh37.p13 chr 4	NC_000004.11:g.170334329_170334336dup
GRCh37.p13 chr 4	NC_000004.11:g.170334323_170334336dup
NEK1 RefSeqGene	NG_027982.1:g.204453_204456del
NEK1 RefSeqGene	NG_027982.1:g.204454_204456del
NEK1 RefSeqGene	NG_027982.1:g.204455_204456del
NEK1 RefSeqGene	NG_027982.1:g.204456del
NEK1 RefSeqGene	NG_027982.1:g.204456dup
NEK1 RefSeqGene	NG_027982.1:g.204455_204456dup
NEK1 RefSeqGene	NG_027982.1:g.204454_204456dup
NEK1 RefSeqGene	NG_027982.1:g.204449_204456dup
NEK1 RefSeqGene	NG_027982.1:g.204443_204456dup

Gene: NEK1, NIMA related kinase 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NEK1 transcript variant 1	NM_001199397.3:c.3223-642… NM_001199397.3:c.3223-6428_3223-6425del	N/A	Intron Variant
NEK1 transcript variant 3	NM_001199398.3:c.3091-642… NM_001199398.3:c.3091-6428_3091-6425del	N/A	Intron Variant
NEK1 transcript variant 4	NM_001199399.3:c.2932-642… NM_001199399.3:c.2932-6428_2932-6425del	N/A	Intron Variant
NEK1 transcript variant 5	NM_001199400.3:c.3007-642… NM_001199400.3:c.3007-6428_3007-6425del	N/A	Intron Variant
NEK1 transcript variant 6	NM_001374418.1:c.3223-642… NM_001374418.1:c.3223-6428_3223-6425del	N/A	Intron Variant
NEK1 transcript variant 7	NM_001374419.1:c.3139-642… NM_001374419.1:c.3139-6428_3139-6425del	N/A	Intron Variant
NEK1 transcript variant 8	NM_001374420.1:c.3088-642… NM_001374420.1:c.3088-6428_3088-6425del	N/A	Intron Variant
NEK1 transcript variant 9	NM_001374421.1:c.2740-642… NM_001374421.1:c.2740-6428_2740-6425del	N/A	Intron Variant
NEK1 transcript variant 2	NM_012224.4:c.3139-6428_3… NM_012224.4:c.3139-6428_3139-6425del	N/A	Intron Variant
NEK1 transcript variant 10	NM_001374422.1:c.	N/A	Genic Downstream Transcript Variant
NEK1 transcript variant 11	NM_001374423.1:c.	N/A	Genic Downstream Transcript Variant
NEK1 transcript variant 12	NR_164630.1:n.	N/A	Intron Variant
NEK1 transcript variant 13	NR_164631.1:n.	N/A	Genic Downstream Transcript Variant
NEK1 transcript variant X3	XM_011532004.2:c.3007-642… XM_011532004.2:c.3007-6428_3007-6425del	N/A	Intron Variant
NEK1 transcript variant X1	XM_047415731.1:c.3091-642… XM_047415731.1:c.3091-6428_3091-6425del	N/A	Intron Variant
NEK1 transcript variant X2	XM_047415732.1:c.3046-642… XM_047415732.1:c.3046-6428_3046-6425del	N/A	Intron Variant
NEK1 transcript variant X4	XM_047415733.1:c.2962-642… XM_047415733.1:c.2962-6428_2962-6425del	N/A	Intron Variant
NEK1 transcript variant X5	XM_047415734.1:c.2962-642… XM_047415734.1:c.2962-6428_2962-6425del	N/A	Intron Variant
NEK1 transcript variant X6	XM_047415735.1:c.2914-642… XM_047415735.1:c.2914-6428_2914-6425del	N/A	Intron Variant
NEK1 transcript variant X7	XM_047415736.1:c.2830-642… XM_047415736.1:c.2830-6428_2830-6425del	N/A	Intron Variant
NEK1 transcript variant X8	XM_047415737.1:c.2602-642… XM_047415737.1:c.2602-6428_2602-6425del	N/A	Intron Variant
NEK1 transcript variant X9	XM_047415738.1:c.2602-642… XM_047415738.1:c.2602-6428_2602-6425del	N/A	Intron Variant
NEK1 transcript variant X10	XM_047415739.1:c.2518-642… XM_047415739.1:c.2518-6428_2518-6425del	N/A	Intron Variant
NEK1 transcript variant X12	XM_011532005.3:c.	N/A	Genic Downstream Transcript Variant
NEK1 transcript variant X11	XM_047415740.1:c.	N/A	Genic Downstream Transcript Variant
NEK1 transcript variant X13	XM_047415741.1:c.	N/A	Genic Downstream Transcript Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	(T)₁₄=	del(T)₄	delTTT	delTT	delT	dupT	dupTT	dupTTT	dup(T)₈	dup(T)₁₄
GRCh38.p14 chr 4	NC_000004.12:g.169413172_169413185=	NC_000004.12:g.169413182_169413185del	NC_000004.12:g.169413183_169413185del	NC_000004.12:g.169413184_169413185del	NC_000004.12:g.169413185del	NC_000004.12:g.169413185dup	NC_000004.12:g.169413184_169413185dup	NC_000004.12:g.169413183_169413185dup	NC_000004.12:g.169413178_169413185dup	NC_000004.12:g.169413172_169413185dup
GRCh37.p13 chr 4	NC_000004.11:g.170334323_170334336=	NC_000004.11:g.170334333_170334336del	NC_000004.11:g.170334334_170334336del	NC_000004.11:g.170334335_170334336del	NC_000004.11:g.170334336del	NC_000004.11:g.170334336dup	NC_000004.11:g.170334335_170334336dup	NC_000004.11:g.170334334_170334336dup	NC_000004.11:g.170334329_170334336dup	NC_000004.11:g.170334323_170334336dup
NEK1 RefSeqGene	NG_027982.1:g.204443_204456=	NG_027982.1:g.204453_204456del	NG_027982.1:g.204454_204456del	NG_027982.1:g.204455_204456del	NG_027982.1:g.204456del	NG_027982.1:g.204456dup	NG_027982.1:g.204455_204456dup	NG_027982.1:g.204454_204456dup	NG_027982.1:g.204449_204456dup	NG_027982.1:g.204443_204456dup
NEK1 transcript variant 1	NM_001199397.1:c.3223-6425=	NM_001199397.1:c.3223-6428_3223-6425del	NM_001199397.1:c.3223-6427_3223-6425del	NM_001199397.1:c.3223-6426_3223-6425del	NM_001199397.1:c.3223-6425del	NM_001199397.1:c.3223-6425dup	NM_001199397.1:c.3223-6426_3223-6425dup	NM_001199397.1:c.3223-6427_3223-6425dup	NM_001199397.1:c.3223-6432_3223-6425dup	NM_001199397.1:c.3223-6438_3223-6425dup
NEK1 transcript variant 1	NM_001199397.3:c.3223-6425=	NM_001199397.3:c.3223-6428_3223-6425del	NM_001199397.3:c.3223-6427_3223-6425del	NM_001199397.3:c.3223-6426_3223-6425del	NM_001199397.3:c.3223-6425del	NM_001199397.3:c.3223-6425dup	NM_001199397.3:c.3223-6426_3223-6425dup	NM_001199397.3:c.3223-6427_3223-6425dup	NM_001199397.3:c.3223-6432_3223-6425dup	NM_001199397.3:c.3223-6438_3223-6425dup
NEK1 transcript variant 3	NM_001199398.1:c.3091-6425=	NM_001199398.1:c.3091-6428_3091-6425del	NM_001199398.1:c.3091-6427_3091-6425del	NM_001199398.1:c.3091-6426_3091-6425del	NM_001199398.1:c.3091-6425del	NM_001199398.1:c.3091-6425dup	NM_001199398.1:c.3091-6426_3091-6425dup	NM_001199398.1:c.3091-6427_3091-6425dup	NM_001199398.1:c.3091-6432_3091-6425dup	NM_001199398.1:c.3091-6438_3091-6425dup
NEK1 transcript variant 3	NM_001199398.3:c.3091-6425=	NM_001199398.3:c.3091-6428_3091-6425del	NM_001199398.3:c.3091-6427_3091-6425del	NM_001199398.3:c.3091-6426_3091-6425del	NM_001199398.3:c.3091-6425del	NM_001199398.3:c.3091-6425dup	NM_001199398.3:c.3091-6426_3091-6425dup	NM_001199398.3:c.3091-6427_3091-6425dup	NM_001199398.3:c.3091-6432_3091-6425dup	NM_001199398.3:c.3091-6438_3091-6425dup
NEK1 transcript variant 4	NM_001199399.1:c.2932-6425=	NM_001199399.1:c.2932-6428_2932-6425del	NM_001199399.1:c.2932-6427_2932-6425del	NM_001199399.1:c.2932-6426_2932-6425del	NM_001199399.1:c.2932-6425del	NM_001199399.1:c.2932-6425dup	NM_001199399.1:c.2932-6426_2932-6425dup	NM_001199399.1:c.2932-6427_2932-6425dup	NM_001199399.1:c.2932-6432_2932-6425dup	NM_001199399.1:c.2932-6438_2932-6425dup
NEK1 transcript variant 4	NM_001199399.3:c.2932-6425=	NM_001199399.3:c.2932-6428_2932-6425del	NM_001199399.3:c.2932-6427_2932-6425del	NM_001199399.3:c.2932-6426_2932-6425del	NM_001199399.3:c.2932-6425del	NM_001199399.3:c.2932-6425dup	NM_001199399.3:c.2932-6426_2932-6425dup	NM_001199399.3:c.2932-6427_2932-6425dup	NM_001199399.3:c.2932-6432_2932-6425dup	NM_001199399.3:c.2932-6438_2932-6425dup
NEK1 transcript variant 5	NM_001199400.1:c.3007-6425=	NM_001199400.1:c.3007-6428_3007-6425del	NM_001199400.1:c.3007-6427_3007-6425del	NM_001199400.1:c.3007-6426_3007-6425del	NM_001199400.1:c.3007-6425del	NM_001199400.1:c.3007-6425dup	NM_001199400.1:c.3007-6426_3007-6425dup	NM_001199400.1:c.3007-6427_3007-6425dup	NM_001199400.1:c.3007-6432_3007-6425dup	NM_001199400.1:c.3007-6438_3007-6425dup
NEK1 transcript variant 5	NM_001199400.3:c.3007-6425=	NM_001199400.3:c.3007-6428_3007-6425del	NM_001199400.3:c.3007-6427_3007-6425del	NM_001199400.3:c.3007-6426_3007-6425del	NM_001199400.3:c.3007-6425del	NM_001199400.3:c.3007-6425dup	NM_001199400.3:c.3007-6426_3007-6425dup	NM_001199400.3:c.3007-6427_3007-6425dup	NM_001199400.3:c.3007-6432_3007-6425dup	NM_001199400.3:c.3007-6438_3007-6425dup
NEK1 transcript variant 6	NM_001374418.1:c.3223-6425=	NM_001374418.1:c.3223-6428_3223-6425del	NM_001374418.1:c.3223-6427_3223-6425del	NM_001374418.1:c.3223-6426_3223-6425del	NM_001374418.1:c.3223-6425del	NM_001374418.1:c.3223-6425dup	NM_001374418.1:c.3223-6426_3223-6425dup	NM_001374418.1:c.3223-6427_3223-6425dup	NM_001374418.1:c.3223-6432_3223-6425dup	NM_001374418.1:c.3223-6438_3223-6425dup
NEK1 transcript variant 7	NM_001374419.1:c.3139-6425=	NM_001374419.1:c.3139-6428_3139-6425del	NM_001374419.1:c.3139-6427_3139-6425del	NM_001374419.1:c.3139-6426_3139-6425del	NM_001374419.1:c.3139-6425del	NM_001374419.1:c.3139-6425dup	NM_001374419.1:c.3139-6426_3139-6425dup	NM_001374419.1:c.3139-6427_3139-6425dup	NM_001374419.1:c.3139-6432_3139-6425dup	NM_001374419.1:c.3139-6438_3139-6425dup
NEK1 transcript variant 8	NM_001374420.1:c.3088-6425=	NM_001374420.1:c.3088-6428_3088-6425del	NM_001374420.1:c.3088-6427_3088-6425del	NM_001374420.1:c.3088-6426_3088-6425del	NM_001374420.1:c.3088-6425del	NM_001374420.1:c.3088-6425dup	NM_001374420.1:c.3088-6426_3088-6425dup	NM_001374420.1:c.3088-6427_3088-6425dup	NM_001374420.1:c.3088-6432_3088-6425dup	NM_001374420.1:c.3088-6438_3088-6425dup
NEK1 transcript variant 9	NM_001374421.1:c.2740-6425=	NM_001374421.1:c.2740-6428_2740-6425del	NM_001374421.1:c.2740-6427_2740-6425del	NM_001374421.1:c.2740-6426_2740-6425del	NM_001374421.1:c.2740-6425del	NM_001374421.1:c.2740-6425dup	NM_001374421.1:c.2740-6426_2740-6425dup	NM_001374421.1:c.2740-6427_2740-6425dup	NM_001374421.1:c.2740-6432_2740-6425dup	NM_001374421.1:c.2740-6438_2740-6425dup
NEK1 transcript variant 2	NM_012224.2:c.3139-6425=	NM_012224.2:c.3139-6428_3139-6425del	NM_012224.2:c.3139-6427_3139-6425del	NM_012224.2:c.3139-6426_3139-6425del	NM_012224.2:c.3139-6425del	NM_012224.2:c.3139-6425dup	NM_012224.2:c.3139-6426_3139-6425dup	NM_012224.2:c.3139-6427_3139-6425dup	NM_012224.2:c.3139-6432_3139-6425dup	NM_012224.2:c.3139-6438_3139-6425dup
NEK1 transcript variant 2	NM_012224.4:c.3139-6425=	NM_012224.4:c.3139-6428_3139-6425del	NM_012224.4:c.3139-6427_3139-6425del	NM_012224.4:c.3139-6426_3139-6425del	NM_012224.4:c.3139-6425del	NM_012224.4:c.3139-6425dup	NM_012224.4:c.3139-6426_3139-6425dup	NM_012224.4:c.3139-6427_3139-6425dup	NM_012224.4:c.3139-6432_3139-6425dup	NM_012224.4:c.3139-6438_3139-6425dup
NEK1 transcript variant X1	XM_005263027.1:c.3139-6425=	XM_005263027.1:c.3139-6428_3139-6425del	XM_005263027.1:c.3139-6427_3139-6425del	XM_005263027.1:c.3139-6426_3139-6425del	XM_005263027.1:c.3139-6425del	XM_005263027.1:c.3139-6425dup	XM_005263027.1:c.3139-6426_3139-6425dup	XM_005263027.1:c.3139-6427_3139-6425dup	XM_005263027.1:c.3139-6432_3139-6425dup	XM_005263027.1:c.3139-6438_3139-6425dup
NEK1 transcript variant X2	XM_005263028.1:c.3007-6425=	XM_005263028.1:c.3007-6428_3007-6425del	XM_005263028.1:c.3007-6427_3007-6425del	XM_005263028.1:c.3007-6426_3007-6425del	XM_005263028.1:c.3007-6425del	XM_005263028.1:c.3007-6425dup	XM_005263028.1:c.3007-6426_3007-6425dup	XM_005263028.1:c.3007-6427_3007-6425dup	XM_005263028.1:c.3007-6432_3007-6425dup	XM_005263028.1:c.3007-6438_3007-6425dup
NEK1 transcript variant X3	XM_011532004.2:c.3007-6425=	XM_011532004.2:c.3007-6428_3007-6425del	XM_011532004.2:c.3007-6427_3007-6425del	XM_011532004.2:c.3007-6426_3007-6425del	XM_011532004.2:c.3007-6425del	XM_011532004.2:c.3007-6425dup	XM_011532004.2:c.3007-6426_3007-6425dup	XM_011532004.2:c.3007-6427_3007-6425dup	XM_011532004.2:c.3007-6432_3007-6425dup	XM_011532004.2:c.3007-6438_3007-6425dup
NEK1 transcript variant X1	XM_047415731.1:c.3091-6425=	XM_047415731.1:c.3091-6428_3091-6425del	XM_047415731.1:c.3091-6427_3091-6425del	XM_047415731.1:c.3091-6426_3091-6425del	XM_047415731.1:c.3091-6425del	XM_047415731.1:c.3091-6425dup	XM_047415731.1:c.3091-6426_3091-6425dup	XM_047415731.1:c.3091-6427_3091-6425dup	XM_047415731.1:c.3091-6432_3091-6425dup	XM_047415731.1:c.3091-6438_3091-6425dup
NEK1 transcript variant X2	XM_047415732.1:c.3046-6425=	XM_047415732.1:c.3046-6428_3046-6425del	XM_047415732.1:c.3046-6427_3046-6425del	XM_047415732.1:c.3046-6426_3046-6425del	XM_047415732.1:c.3046-6425del	XM_047415732.1:c.3046-6425dup	XM_047415732.1:c.3046-6426_3046-6425dup	XM_047415732.1:c.3046-6427_3046-6425dup	XM_047415732.1:c.3046-6432_3046-6425dup	XM_047415732.1:c.3046-6438_3046-6425dup
NEK1 transcript variant X4	XM_047415733.1:c.2962-6425=	XM_047415733.1:c.2962-6428_2962-6425del	XM_047415733.1:c.2962-6427_2962-6425del	XM_047415733.1:c.2962-6426_2962-6425del	XM_047415733.1:c.2962-6425del	XM_047415733.1:c.2962-6425dup	XM_047415733.1:c.2962-6426_2962-6425dup	XM_047415733.1:c.2962-6427_2962-6425dup	XM_047415733.1:c.2962-6432_2962-6425dup	XM_047415733.1:c.2962-6438_2962-6425dup
NEK1 transcript variant X5	XM_047415734.1:c.2962-6425=	XM_047415734.1:c.2962-6428_2962-6425del	XM_047415734.1:c.2962-6427_2962-6425del	XM_047415734.1:c.2962-6426_2962-6425del	XM_047415734.1:c.2962-6425del	XM_047415734.1:c.2962-6425dup	XM_047415734.1:c.2962-6426_2962-6425dup	XM_047415734.1:c.2962-6427_2962-6425dup	XM_047415734.1:c.2962-6432_2962-6425dup	XM_047415734.1:c.2962-6438_2962-6425dup
NEK1 transcript variant X6	XM_047415735.1:c.2914-6425=	XM_047415735.1:c.2914-6428_2914-6425del	XM_047415735.1:c.2914-6427_2914-6425del	XM_047415735.1:c.2914-6426_2914-6425del	XM_047415735.1:c.2914-6425del	XM_047415735.1:c.2914-6425dup	XM_047415735.1:c.2914-6426_2914-6425dup	XM_047415735.1:c.2914-6427_2914-6425dup	XM_047415735.1:c.2914-6432_2914-6425dup	XM_047415735.1:c.2914-6438_2914-6425dup
NEK1 transcript variant X7	XM_047415736.1:c.2830-6425=	XM_047415736.1:c.2830-6428_2830-6425del	XM_047415736.1:c.2830-6427_2830-6425del	XM_047415736.1:c.2830-6426_2830-6425del	XM_047415736.1:c.2830-6425del	XM_047415736.1:c.2830-6425dup	XM_047415736.1:c.2830-6426_2830-6425dup	XM_047415736.1:c.2830-6427_2830-6425dup	XM_047415736.1:c.2830-6432_2830-6425dup	XM_047415736.1:c.2830-6438_2830-6425dup
NEK1 transcript variant X8	XM_047415737.1:c.2602-6425=	XM_047415737.1:c.2602-6428_2602-6425del	XM_047415737.1:c.2602-6427_2602-6425del	XM_047415737.1:c.2602-6426_2602-6425del	XM_047415737.1:c.2602-6425del	XM_047415737.1:c.2602-6425dup	XM_047415737.1:c.2602-6426_2602-6425dup	XM_047415737.1:c.2602-6427_2602-6425dup	XM_047415737.1:c.2602-6432_2602-6425dup	XM_047415737.1:c.2602-6438_2602-6425dup
NEK1 transcript variant X9	XM_047415738.1:c.2602-6425=	XM_047415738.1:c.2602-6428_2602-6425del	XM_047415738.1:c.2602-6427_2602-6425del	XM_047415738.1:c.2602-6426_2602-6425del	XM_047415738.1:c.2602-6425del	XM_047415738.1:c.2602-6425dup	XM_047415738.1:c.2602-6426_2602-6425dup	XM_047415738.1:c.2602-6427_2602-6425dup	XM_047415738.1:c.2602-6432_2602-6425dup	XM_047415738.1:c.2602-6438_2602-6425dup
NEK1 transcript variant X10	XM_047415739.1:c.2518-6425=	XM_047415739.1:c.2518-6428_2518-6425del	XM_047415739.1:c.2518-6427_2518-6425del	XM_047415739.1:c.2518-6426_2518-6425del	XM_047415739.1:c.2518-6425del	XM_047415739.1:c.2518-6425dup	XM_047415739.1:c.2518-6426_2518-6425dup	XM_047415739.1:c.2518-6427_2518-6425dup	XM_047415739.1:c.2518-6432_2518-6425dup	XM_047415739.1:c.2518-6438_2518-6425dup

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

57 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss82573367	Sep 08, 2015 (146)
2	HUMANGENOME_JCVI	ss95377805	Feb 05, 2009 (137)
3	BUSHMAN	ss193773759	Jul 04, 2010 (137)
4	GMI	ss288596400	May 04, 2012 (137)
5	PJP	ss295200456	May 09, 2011 (137)
6	SSMP	ss663480609	Apr 01, 2015 (144)
7	BILGI_BIOE	ss666288659	Apr 25, 2013 (138)
8	EVA-GONL	ss980976084	Aug 21, 2014 (142)
9	1000GENOMES	ss1373114969	Aug 21, 2014 (142)
10	DDI	ss1536440627	Apr 01, 2015 (144)
11	EVA_GENOME_DK	ss1576397700	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1704465244	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1704466902	Apr 01, 2015 (144)
14	JJLAB	ss2030648629	Sep 14, 2016 (149)
15	SYSTEMSBIOZJU	ss2625844138	Nov 08, 2017 (151)
16	SWEGEN	ss2996007612	Nov 08, 2017 (151)
17	MCHAISSO	ss3064134657	Nov 08, 2017 (151)
18	MCHAISSO	ss3065003243	Nov 08, 2017 (151)
19	MCHAISSO	ss3065989115	Nov 08, 2017 (151)
20	BEROUKHIMLAB	ss3644171823	Oct 12, 2018 (152)
21	BIOINF_KMB_FNS_UNIBA	ss3645843564	Oct 12, 2018 (152)
22	URBANLAB	ss3647915503	Oct 12, 2018 (152)
23	EVA_DECODE	ss3713607934	Jul 13, 2019 (153)
24	EVA_DECODE	ss3713607935	Jul 13, 2019 (153)
25	EVA_DECODE	ss3713607936	Jul 13, 2019 (153)
26	EVA_DECODE	ss3713607937	Jul 13, 2019 (153)
27	EVA_DECODE	ss3713607938	Jul 13, 2019 (153)
28	ACPOP	ss3731854291	Jul 13, 2019 (153)
29	PACBIO	ss3784942117	Jul 13, 2019 (153)
30	PACBIO	ss3790367036	Jul 13, 2019 (153)
31	PACBIO	ss3795242720	Jul 13, 2019 (153)
32	KHV_HUMAN_GENOMES	ss3805915597	Jul 13, 2019 (153)
33	EVA	ss3828953940	Apr 26, 2020 (154)
34	EVA	ss3837929475	Apr 26, 2020 (154)
35	EVA	ss3843370855	Apr 26, 2020 (154)
36	KOGIC	ss3955641143	Apr 26, 2020 (154)
37	KOGIC	ss3955641144	Apr 26, 2020 (154)
38	GNOMAD	ss4125272018	Apr 26, 2021 (155)
39	GNOMAD	ss4125272019	Apr 26, 2021 (155)
40	GNOMAD	ss4125272020	Apr 26, 2021 (155)
41	GNOMAD	ss4125272021	Apr 26, 2021 (155)
42	GNOMAD	ss4125272022	Apr 26, 2021 (155)
43	GNOMAD	ss4125272023	Apr 26, 2021 (155)
44	TOMMO_GENOMICS	ss5169264194	Apr 26, 2021 (155)
45	TOMMO_GENOMICS	ss5169264195	Apr 26, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5262000307	Oct 13, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5262000308	Oct 13, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5262000309	Oct 13, 2022 (156)
49	HUGCELL_USP	ss5460450232	Oct 13, 2022 (156)
50	HUGCELL_USP	ss5460450233	Oct 13, 2022 (156)
51	TOMMO_GENOMICS	ss5704602957	Oct 13, 2022 (156)
52	TOMMO_GENOMICS	ss5704602958	Oct 13, 2022 (156)
53	YY_MCH	ss5805785196	Oct 13, 2022 (156)
54	EVA	ss5845100575	Oct 13, 2022 (156)
55	EVA	ss5854564619	Oct 13, 2022 (156)
56	EVA	ss5866615363	Oct 13, 2022 (156)
57	EVA	ss5965076663	Oct 13, 2022 (156)
58	1000Genomes	NC_000004.11 - 170334323	Oct 12, 2018 (152)
59	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 170334323	Oct 12, 2018 (152)
60	The Danish reference pan genome	NC_000004.11 - 170334323	Apr 26, 2020 (154)
61	gnomAD - Genomes Submission ignored due to conflicting rows: Row 173102022 (NC_000004.12:169413171::T 3652/132972) Row 173102023 (NC_000004.12:169413171::TT 1/133004) Row 173102024 (NC_000004.12:169413171:T: 105705/132898)...	-	Apr 26, 2021 (155)
62	gnomAD - Genomes Submission ignored due to conflicting rows: Row 173102022 (NC_000004.12:169413171::T 3652/132972) Row 173102023 (NC_000004.12:169413171::TT 1/133004) Row 173102024 (NC_000004.12:169413171:T: 105705/132898)...	-	Apr 26, 2021 (155)
63	gnomAD - Genomes Submission ignored due to conflicting rows: Row 173102022 (NC_000004.12:169413171::T 3652/132972) Row 173102023 (NC_000004.12:169413171::TT 1/133004) Row 173102024 (NC_000004.12:169413171:T: 105705/132898)...	-	Apr 26, 2021 (155)
64	gnomAD - Genomes Submission ignored due to conflicting rows: Row 173102022 (NC_000004.12:169413171::T 3652/132972) Row 173102023 (NC_000004.12:169413171::TT 1/133004) Row 173102024 (NC_000004.12:169413171:T: 105705/132898)...	-	Apr 26, 2021 (155)
65	gnomAD - Genomes Submission ignored due to conflicting rows: Row 173102022 (NC_000004.12:169413171::T 3652/132972) Row 173102023 (NC_000004.12:169413171::TT 1/133004) Row 173102024 (NC_000004.12:169413171:T: 105705/132898)...	-	Apr 26, 2021 (155)
66	gnomAD - Genomes Submission ignored due to conflicting rows: Row 173102022 (NC_000004.12:169413171::T 3652/132972) Row 173102023 (NC_000004.12:169413171::TT 1/133004) Row 173102024 (NC_000004.12:169413171:T: 105705/132898)...	-	Apr 26, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000004.11 - 170334323	Apr 26, 2020 (154)
68	Korean Genome Project Submission ignored due to conflicting rows: Row 12019144 (NC_000004.12:169413171:TT: 25/1832) Row 12019145 (NC_000004.12:169413172:T: 1478/1832)	-	Apr 26, 2020 (154)
69	Korean Genome Project Submission ignored due to conflicting rows: Row 12019144 (NC_000004.12:169413171:TT: 25/1832) Row 12019145 (NC_000004.12:169413172:T: 1478/1832)	-	Apr 26, 2020 (154)
70	Northern Sweden	NC_000004.11 - 170334323	Jul 13, 2019 (153)
71	8.3KJPN Submission ignored due to conflicting rows: Row 27233501 (NC_000004.11:170334322:T: 14513/16760) Row 27233502 (NC_000004.11:170334322:TT: 13/16760)	-	Apr 26, 2021 (155)
72	8.3KJPN Submission ignored due to conflicting rows: Row 27233501 (NC_000004.11:170334322:T: 14513/16760) Row 27233502 (NC_000004.11:170334322:TT: 13/16760)	-	Apr 26, 2021 (155)
73	14KJPN Submission ignored due to conflicting rows: Row 38440061 (NC_000004.12:169413171:T: 24360/28258) Row 38440062 (NC_000004.12:169413171:TT: 18/28258)	-	Oct 13, 2022 (156)
74	14KJPN Submission ignored due to conflicting rows: Row 38440061 (NC_000004.12:169413171:T: 24360/28258) Row 38440062 (NC_000004.12:169413171:TT: 18/28258)	-	Oct 13, 2022 (156)
75	UK 10K study - Twins	NC_000004.11 - 170334323	Oct 12, 2018 (152)
76	ALFA	NC_000004.12 - 169413172	Apr 26, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID	History Updated (Build)
rs35156597	May 11, 2012 (137)
rs59697464	May 11, 2012 (137)
rs113444145	May 11, 2012 (137)
rs367656760	May 13, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss4125272023	NC_000004.12:169413171:TTTT:	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTT	(self)
3358745473	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTT	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTT	(self)
ss4125272022	NC_000004.12:169413171:TTT:	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTT	(self)
ss5169264195	NC_000004.11:170334322:TT:	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTT	(self)
ss3713607934, ss3955641143, ss4125272021, ss5262000309, ss5704602958	NC_000004.12:169413171:TT:	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTT	(self)
3358745473	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTT	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTT	(self)
ss82573367	NC_000004.9:170709065:T:	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
ss288596400, ss295200456	NC_000004.10:170570897:T:	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
24445813, 13598809, 961793, 6026381, 5139156, 13598809, ss663480609, ss666288659, ss980976084, ss1373114969, ss1536440627, ss1576397700, ss1704465244, ss1704466902, ss2030648629, ss2625844138, ss2996007612, ss3644171823, ss3731854291, ss3784942117, ss3790367036, ss3795242720, ss3828953940, ss3837929475, ss5169264194, ss5845100575, ss5965076663	NC_000004.11:170334322:T:	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
ss3064134657, ss3065003243, ss3065989115, ss3645843564, ss3647915503, ss3805915597, ss3843370855, ss4125272020, ss5262000307, ss5460450232, ss5704602957, ss5805785196, ss5854564619, ss5866615363	NC_000004.12:169413171:T:	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
3358745473	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTT	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
ss3713607935, ss3955641144	NC_000004.12:169413172:T:	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
ss95377805	NT_016354.19:94882056:T:	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
ss193773759	NT_016354.20:110491790:T:	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
ss4125272018, ss5262000308, ss5460450233	NC_000004.12:169413171::T	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTT	(self)
3358745473	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTT	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTT	(self)
ss4125272019	NC_000004.12:169413171::TT	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTTT	(self)
3358745473	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTTT	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTTT	(self)
ss3713607936	NC_000004.12:169413173::TTT	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT	(self)
ss3713607937	NC_000004.12:169413173::TTTTTTTT	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTT	(self)
ss3713607938	NC_000004.12:169413173::TTTTTTTTTT… NC_000004.12:169413173::TTTTTTTTTTTTTT	NC_000004.12:169413171:TTTTTTTTTTT… NC_000004.12:169413171:TTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTTTTTTTT	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs5863996

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs5863996