Name: rs1489435177
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.

rs1489435177

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:49557255-49557269 (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: dupAAT
Variation Type: Indel Insertion and Deletion
Frequency: dupAAT=0.000057 (8/140178, GnomAD)
dupAAT=0.00004 (1/28258, 14KJPN)
dupAAT=0.00006 (1/16760, 8.3KJPN) (+ 2 more)
dupAAT=0.00017 (2/11862, ALFA)
dupAAT=0.0003 (2/6404, 1000G_30x)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: C6orf141 : 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	HTRZ	HWEP
Total	Global	11862	AATAATAATAATAAT=0.99983	AATAATAATAATAATAAT=0.00017	0.999663	0.000337	0
European	Sub	7618	AATAATAATAATAAT=0.9999	AATAATAATAATAATAAT=0.0001	0.999737	0.000263	0
African	Sub	2816	AATAATAATAATAAT=0.9996	AATAATAATAATAATAAT=0.0004	0.99929	0.00071	0
African Others	Sub	108	AATAATAATAATAAT=1.000	AATAATAATAATAATAAT=0.000	1.0	0.0	N/A
African American	Sub	2708	AATAATAATAATAAT=0.9996	AATAATAATAATAATAAT=0.0004	0.999261	0.000739	0
Asian	Sub	108	AATAATAATAATAAT=1.000	AATAATAATAATAATAAT=0.000	1.0	0.0	N/A
East Asian	Sub	84	AATAATAATAATAAT=1.00	AATAATAATAATAATAAT=0.00	1.0	0.0	N/A
Other Asian	Sub	24	AATAATAATAATAAT=1.00	AATAATAATAATAATAAT=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	AATAATAATAATAAT=1.000	AATAATAATAATAATAAT=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	AATAATAATAATAAT=1.000	AATAATAATAATAATAAT=0.000	1.0	0.0	N/A
South Asian	Sub	94	AATAATAATAATAAT=1.00	AATAATAATAATAATAAT=0.00	1.0	0.0	N/A
Other	Sub	470	AATAATAATAATAAT=1.000	AATAATAATAATAATAAT=0.000	1.0	0.0	N/A

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
gnomAD - Genomes	Global	Study-wide	140178	- No frequency provided	dupAAT=0.000057
gnomAD - Genomes	European	Sub	75932	- No frequency provided	dupAAT=0.00008
gnomAD - Genomes	African	Sub	42004	- No frequency provided	dupAAT=0.00002
gnomAD - Genomes	American	Sub	13640	- No frequency provided	dupAAT=0.00007
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	- No frequency provided	dupAAT=0.0000
gnomAD - Genomes	East Asian	Sub	3134	- No frequency provided	dupAAT=0.0000
gnomAD - Genomes	Other	Sub	2148	- No frequency provided	dupAAT=0.0000
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	dupAAT=0.00004
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupAAT=0.00006
Allele Frequency Aggregator	Total	Global	11862	(AAT)₅=0.99983	dupAAT=0.00017
Allele Frequency Aggregator	European	Sub	7618	(AAT)₅=0.9999	dupAAT=0.0001
Allele Frequency Aggregator	African	Sub	2816	(AAT)₅=0.9996	dupAAT=0.0004
Allele Frequency Aggregator	Latin American 2	Sub	610	(AAT)₅=1.000	dupAAT=0.000
Allele Frequency Aggregator	Other	Sub	470	(AAT)₅=1.000	dupAAT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(AAT)₅=1.000	dupAAT=0.000
Allele Frequency Aggregator	Asian	Sub	108	(AAT)₅=1.000	dupAAT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	(AAT)₅=1.00	dupAAT=0.00
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	dupAAT=0.0003
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupAAT=0.0000
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupAAT=0.0000
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupAAT=0.0000
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupAAT=0.0000
1000Genomes_30x	American	Sub	980	- No frequency provided	dupAAT=0.002

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 6	NC_000006.12:g.49557255AAT[6]
GRCh37.p13 chr 6	NC_000006.11:g.49524968AAT[6]

Gene: C6orf141, chromosome 6 open reading frame 141 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
C6orf141 transcript variant 1	NM_001145652.2:c.	N/A	Genic Downstream Transcript Variant
C6orf141 transcript variant 2	NR_146853.2:n.	N/A	Intron Variant
C6orf141 transcript variant 3	NR_146854.3:n.	N/A	Intron Variant
C6orf141 transcript variant 4	NR_146855.2:n.	N/A	Intron Variant
C6orf141 transcript variant 5	NR_146856.3:n.	N/A	Intron Variant
C6orf141 transcript variant 6	NR_146857.3:n.	N/A	Intron Variant
C6orf141 transcript variant 7	NR_146858.2:n.	N/A	Intron Variant
C6orf141 transcript variant 8	NR_146859.3:n.	N/A	Intron Variant
C6orf141 transcript variant 9	NR_146860.3:n.	N/A	Intron Variant
C6orf141 transcript variant 10	NR_146861.2:n.	N/A	Intron Variant
C6orf141 transcript variant 11	NR_146862.3:n.	N/A	Intron Variant
C6orf141 transcript variant 12	NR_146863.2:n.	N/A	Intron Variant
C6orf141 transcript variant 13	NR_146864.3:n.	N/A	Intron Variant
C6orf141 transcript	NR_170563.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170564.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170565.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170566.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170567.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170568.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170569.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170570.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170571.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170572.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170573.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170574.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170575.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170576.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170577.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170578.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170579.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170580.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170581.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170582.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170583.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170584.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170585.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170586.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170587.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170588.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170589.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170590.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170591.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170592.1:n.	N/A	Intron Variant
C6orf141 transcript	NR_170593.1:n.	N/A	Intron Variant
C6orf141 transcript variant X4	XM_047418226.1:c.3019+20… XM_047418226.1:c.3019+2098AAT[6]	N/A	Intron Variant
C6orf141 transcript variant X6	XM_047418229.1:c.3124+20… XM_047418229.1:c.3124+2098AAT[6]	N/A	Intron Variant
C6orf141 transcript variant X8	XM_047418230.1:c.666+209… XM_047418230.1:c.666+2098AAT[6]	N/A	Intron Variant
C6orf141 transcript variant X1	XM_005248850.4:c.	N/A	Genic Downstream Transcript Variant
C6orf141 transcript variant X7	XM_005248853.3:c.	N/A	Genic Downstream Transcript Variant
C6orf141 transcript variant X2	XM_006714997.3:c.	N/A	Genic Downstream Transcript Variant
C6orf141 transcript variant X3	XM_047418225.1:c.	N/A	Genic Downstream Transcript Variant
C6orf141 transcript variant X9	XM_047418227.1:c.	N/A	Genic Downstream Transcript Variant
C6orf141 transcript variant X5	XM_047418228.1:c.	N/A	Genic Downstream Transcript Variant
C6orf141 transcript variant X10	XM_047418231.1: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	(AAT)₅=	dupAAT
GRCh38.p14 chr 6	NC_000006.12:g.49557255_49557269=	NC_000006.12:g.49557255AAT[6]
GRCh37.p13 chr 6	NC_000006.11:g.49524968_49524982=	NC_000006.11:g.49524968AAT[6]
C6orf141 transcript variant X4	XM_047418226.1:c.*3019+2098=	XM_047418226.1:c.*3019+2098AAT[6]
C6orf141 transcript variant X6	XM_047418229.1:c.*3124+2098=	XM_047418229.1:c.*3124+2098AAT[6]
C6orf141 transcript variant X8	XM_047418230.1:c.*666+2098=	XM_047418230.1:c.*666+2098AAT[6]

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#.

5 SubSNP, 5 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2838878978	Nov 08, 2017 (151)
2	TOMMO_GENOMICS	ss5177455351	Apr 26, 2021 (155)
3	1000G_HIGH_COVERAGE	ss5268408538	Oct 13, 2022 (156)
4	1000G_HIGH_COVERAGE	ss5554286446	Oct 13, 2022 (156)
5	TOMMO_GENOMICS	ss5715487410	Oct 13, 2022 (156)
6	1000Genomes_30x	NC_000006.12 - 49557255	Oct 13, 2022 (156)
7	gnomAD - Genomes	NC_000006.12 - 49557255	Apr 26, 2021 (155)
8	8.3KJPN	NC_000006.11 - 49524968	Apr 26, 2021 (155)
9	14KJPN	NC_000006.12 - 49557255	Oct 13, 2022 (156)
10	ALFA	NC_000006.12 - 49557255	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
35424658, ss2838878978, ss5177455351	NC_000006.11:49524967::AAT	NC_000006.12:49557254:AATAATAATAAT… NC_000006.12:49557254:AATAATAATAATAAT:AATAATAATAATAATAAT	(self)
41812381, 224885071, 49324514, ss5268408538, ss5554286446, ss5715487410	NC_000006.12:49557254::AAT	NC_000006.12:49557254:AATAATAATAAT… NC_000006.12:49557254:AATAATAATAATAAT:AATAATAATAATAATAAT	(self)
1824833682	NC_000006.12:49557254:AATAATAATAAT… NC_000006.12:49557254:AATAATAATAATAAT:AATAATAATAATAATAAT	NC_000006.12:49557254:AATAATAATAAT… NC_000006.12:49557254:AATAATAATAATAAT:AATAATAATAATAATAAT	(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 rs1489435177

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

rs1489435177