Name: rs201369181
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.

rs201369181

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:26585639-26585649 (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: delTA / dupTA
Variation Type: Indel Insertion and Deletion
Frequency: dupTA=0.06456 (1824/28254, 14KJPN)
dupTA=0.06331 (1061/16760, 8.3KJPN)
delTA=0.00000 (0/14030, ALFA) (+ 5 more)
dupTA=0.00000 (0/14030, ALFA)
dupTA=0.0078 (50/6404, 1000G_30x)
dupTA=0.0048 (24/5008, 1000G)
dupTA=0.0628 (115/1830, Korea1K)
dupTA=0.009 (2/216, Vietnamese)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NOVA1 : 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	HWEP
Total	Global	14030	ATATATATATA=1.00000	ATATATATA=0.00000, ATATATATATATA=0.00000	1.0	N/A
European	Sub	9690	ATATATATATA=1.0000	ATATATATA=0.0000, ATATATATATATA=0.0000	1.0	N/A
African	Sub	2886	ATATATATATA=1.0000	ATATATATA=0.0000, ATATATATATATA=0.0000	1.0	N/A
African Others	Sub	114	ATATATATATA=1.000	ATATATATA=0.000, ATATATATATATA=0.000	1.0	N/A
African American	Sub	2772	ATATATATATA=1.0000	ATATATATA=0.0000, ATATATATATATA=0.0000	1.0	N/A
Asian	Sub	106	ATATATATATA=1.000	ATATATATA=0.000, ATATATATATATA=0.000	1.0	N/A
East Asian	Sub	80	ATATATATATA=1.00	ATATATATA=0.00, ATATATATATATA=0.00	1.0	N/A
Other Asian	Sub	26	ATATATATATA=1.00	ATATATATA=0.00, ATATATATATATA=0.00	1.0	N/A
Latin American 1	Sub	146	ATATATATATA=1.000	ATATATATA=0.000, ATATATATATATA=0.000	1.0	N/A
Latin American 2	Sub	610	ATATATATATA=1.000	ATATATATA=0.000, ATATATATATATA=0.000	1.0	N/A
South Asian	Sub	98	ATATATATATA=1.00	ATATATATA=0.00, ATATATATATATA=0.00	1.0	N/A
Other	Sub	494	ATATATATATA=1.000	ATATATATA=0.000, ATATATATATATA=0.000	1.0	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
14KJPN	JAPANESE	Study-wide	28254	- No frequency provided	dupTA=0.06456
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupTA=0.06331
Allele Frequency Aggregator	Total	Global	14030	(AT)₅A=1.00000	delTA=0.00000, dupTA=0.00000
Allele Frequency Aggregator	European	Sub	9690	(AT)₅A=1.0000	delTA=0.0000, dupTA=0.0000
Allele Frequency Aggregator	African	Sub	2886	(AT)₅A=1.0000	delTA=0.0000, dupTA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(AT)₅A=1.000	delTA=0.000, dupTA=0.000
Allele Frequency Aggregator	Other	Sub	494	(AT)₅A=1.000	delTA=0.000, dupTA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(AT)₅A=1.000	delTA=0.000, dupTA=0.000
Allele Frequency Aggregator	Asian	Sub	106	(AT)₅A=1.000	delTA=0.000, dupTA=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(AT)₅A=1.00	delTA=0.00, dupTA=0.00
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	dupTA=0.0078
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupTA=0.0006
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupTA=0.0016
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupTA=0.0008
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupTA=0.0393
1000Genomes_30x	American	Sub	980	- No frequency provided	dupTA=0.000
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupTA=0.0048
1000Genomes	African	Sub	1322	- No frequency provided	dupTA=0.0008
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupTA=0.0218
1000Genomes	Europe	Sub	1006	- No frequency provided	dupTA=0.0010
1000Genomes	South Asian	Sub	978	- No frequency provided	dupTA=0.000
1000Genomes	American	Sub	694	- No frequency provided	dupTA=0.000
Korean Genome Project	KOREAN	Study-wide	1830	- No frequency provided	dupTA=0.0628
A Vietnamese Genetic Variation Database	Global	Study-wide	216	- No frequency provided	dupTA=0.009

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 14	NC_000014.9:g.26585640TA[4]
GRCh38.p14 chr 14	NC_000014.9:g.26585640TA[6]
GRCh37.p13 chr 14	NC_000014.8:g.27054846TA[4]
GRCh37.p13 chr 14	NC_000014.8:g.27054846TA[6]

Gene: NOVA1, NOVA alternative splicing regulator 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NOVA1 transcript variant 4	NM_001366390.2:c.-189+976… NM_001366390.2:c.-189+9762AT[4]	N/A	Intron Variant
NOVA1 transcript variant 5	NM_001366391.2:c.-189+976… NM_001366391.2:c.-189+9762AT[4]	N/A	Intron Variant
NOVA1 transcript variant 6	NM_001366392.2:c.277+9762… NM_001366392.2:c.277+9762AT[4]	N/A	Intron Variant
NOVA1 transcript variant 7	NM_001366393.2:c.169+9762… NM_001366393.2:c.169+9762AT[4]	N/A	Intron Variant
NOVA1 transcript variant 8	NM_001366394.2:c.169+9762… NM_001366394.2:c.169+9762AT[4]	N/A	Intron Variant
NOVA1 transcript variant 9	NM_001366395.2:c.-189+976… NM_001366395.2:c.-189+9762AT[4]	N/A	Intron Variant
NOVA1 transcript variant 10	NM_001366396.2:c.-189+976… NM_001366396.2:c.-189+9762AT[4]	N/A	Intron Variant
NOVA1 transcript variant 11	NM_001366397.2:c.-87+9762… NM_001366397.2:c.-87+9762AT[4]	N/A	Intron Variant
NOVA1 transcript variant 1	NM_002515.3:c.280+9762AT[… NM_002515.3:c.280+9762AT[4]	N/A	Intron Variant
NOVA1 transcript variant 2	NM_006489.3:c.280+9762AT[… NM_006489.3:c.280+9762AT[4]	N/A	Intron Variant
NOVA1 transcript variant 3	NM_006491.3:c.280+9762AT[… NM_006491.3:c.280+9762AT[4]	N/A	Intron Variant
NOVA1 transcript variant 12	NM_001366398.2:c.	N/A	Genic Upstream Transcript Variant
NOVA1 transcript variant X1	XM_017021345.2:c.-87+9762… XM_017021345.2:c.-87+9762AT[4]	N/A	Intron 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	(AT)₅A=	delTA	dupTA
GRCh38.p14 chr 14	NC_000014.9:g.26585639_26585649=	NC_000014.9:g.26585640TA[4]	NC_000014.9:g.26585640TA[6]
GRCh37.p13 chr 14	NC_000014.8:g.27054845_27054855=	NC_000014.8:g.27054846TA[4]	NC_000014.8:g.27054846TA[6]
NOVA1 transcript variant 4	NM_001366390.2:c.-189+9771=	NM_001366390.2:c.-189+9762AT[4]	NM_001366390.2:c.-189+9762AT[6]
NOVA1 transcript variant 5	NM_001366391.2:c.-189+9771=	NM_001366391.2:c.-189+9762AT[4]	NM_001366391.2:c.-189+9762AT[6]
NOVA1 transcript variant 6	NM_001366392.2:c.277+9771=	NM_001366392.2:c.277+9762AT[4]	NM_001366392.2:c.277+9762AT[6]
NOVA1 transcript variant 7	NM_001366393.2:c.169+9771=	NM_001366393.2:c.169+9762AT[4]	NM_001366393.2:c.169+9762AT[6]
NOVA1 transcript variant 8	NM_001366394.2:c.169+9771=	NM_001366394.2:c.169+9762AT[4]	NM_001366394.2:c.169+9762AT[6]
NOVA1 transcript variant 9	NM_001366395.2:c.-189+9771=	NM_001366395.2:c.-189+9762AT[4]	NM_001366395.2:c.-189+9762AT[6]
NOVA1 transcript variant 10	NM_001366396.2:c.-189+9771=	NM_001366396.2:c.-189+9762AT[4]	NM_001366396.2:c.-189+9762AT[6]
NOVA1 transcript variant 11	NM_001366397.2:c.-87+9771=	NM_001366397.2:c.-87+9762AT[4]	NM_001366397.2:c.-87+9762AT[6]
NOVA1 transcript variant 1	NM_002515.2:c.280+9771=	NM_002515.2:c.280+9762AT[4]	NM_002515.2:c.280+9762AT[6]
NOVA1 transcript variant 1	NM_002515.3:c.280+9771=	NM_002515.3:c.280+9762AT[4]	NM_002515.3:c.280+9762AT[6]
NOVA1 transcript variant 2	NM_006489.2:c.280+9771=	NM_006489.2:c.280+9762AT[4]	NM_006489.2:c.280+9762AT[6]
NOVA1 transcript variant 2	NM_006489.3:c.280+9771=	NM_006489.3:c.280+9762AT[4]	NM_006489.3:c.280+9762AT[6]
NOVA1 transcript variant 3	NM_006491.2:c.280+9771=	NM_006491.2:c.280+9762AT[4]	NM_006491.2:c.280+9762AT[6]
NOVA1 transcript variant 3	NM_006491.3:c.280+9771=	NM_006491.3:c.280+9762AT[4]	NM_006491.3:c.280+9762AT[6]
NOVA1 transcript variant X1	XM_005267706.1:c.169+9771=	XM_005267706.1:c.169+9762AT[4]	XM_005267706.1:c.169+9762AT[6]
NOVA1 transcript variant X2	XM_005267707.1:c.-189+9771=	XM_005267707.1:c.-189+9762AT[4]	XM_005267707.1:c.-189+9762AT[6]
NOVA1 transcript variant X1	XM_017021345.2:c.-87+9771=	XM_017021345.2:c.-87+9762AT[4]	XM_017021345.2:c.-87+9762AT[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#.

20 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss289210020	Oct 12, 2018 (152)
2	1000GENOMES	ss500133970	May 04, 2012 (137)
3	LUNTER	ss553541361	Apr 25, 2013 (138)
4	SSMP	ss664216715	Apr 01, 2015 (144)
5	1000GENOMES	ss1373849603	Aug 21, 2014 (142)
6	GNOMAD	ss2925631070	Nov 08, 2017 (151)
7	KHV_HUMAN_GENOMES	ss3817436203	Jul 13, 2019 (153)
8	KOGIC	ss3974578479	Apr 27, 2020 (154)
9	GNOMAD	ss4274893184	Apr 26, 2021 (155)
10	TOPMED	ss4964357092	Apr 26, 2021 (155)
11	TOPMED	ss4964357093	Apr 26, 2021 (155)
12	TOMMO_GENOMICS	ss5212416746	Apr 26, 2021 (155)
13	1000G_HIGH_COVERAGE	ss5295585283	Oct 16, 2022 (156)
14	HUGCELL_USP	ss5489705372	Oct 16, 2022 (156)
15	1000G_HIGH_COVERAGE	ss5595529921	Oct 16, 2022 (156)
16	SANFORD_IMAGENETICS	ss5655852446	Oct 16, 2022 (156)
17	TOMMO_GENOMICS	ss5764985347	Oct 16, 2022 (156)
18	YY_MCH	ss5814593846	Oct 16, 2022 (156)
19	EVA	ss5900619676	Oct 16, 2022 (156)
20	EVA	ss5947271183	Oct 16, 2022 (156)
21	1000Genomes	NC_000014.8 - 27054845	Oct 12, 2018 (152)
22	1000Genomes_30x	NC_000014.9 - 26585639	Oct 16, 2022 (156)
23	gnomAD - Genomes Submission ignored due to conflicting rows: Row 445907215 (NC_000014.9:26585638::AT 141/139390) Row 445907216 (NC_000014.9:26585638:AT: 1/139392)	-	Apr 26, 2021 (155)
24	gnomAD - Genomes Submission ignored due to conflicting rows: Row 445907215 (NC_000014.9:26585638::AT 141/139390) Row 445907216 (NC_000014.9:26585638:AT: 1/139392)	-	Apr 26, 2021 (155)
25	Korean Genome Project	NC_000014.9 - 26585639	Apr 27, 2020 (154)
26	8.3KJPN	NC_000014.8 - 27054845	Apr 26, 2021 (155)
27	14KJPN	NC_000014.9 - 26585639	Oct 16, 2022 (156)
28	TopMed Submission ignored due to conflicting rows: Row 179902751 (NC_000014.9:26585638::AT 432/264690) Row 179902752 (NC_000014.9:26585638:AT: 1/264690)	-	Apr 26, 2021 (155)
29	TopMed Submission ignored due to conflicting rows: Row 179902751 (NC_000014.9:26585638::AT 432/264690) Row 179902752 (NC_000014.9:26585638:AT: 1/264690)	-	Apr 26, 2021 (155)
30	A Vietnamese Genetic Variation Database	NC_000014.8 - 27054845	Jul 13, 2019 (153)
31	ALFA	NC_000014.9 - 26585639	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
ss4274893184, ss4964357093	NC_000014.9:26585638:AT:	NC_000014.9:26585638:ATATATATATA:A… NC_000014.9:26585638:ATATATATATA:ATATATATA	(self)
4864515870	NC_000014.9:26585638:ATATATATATA:A… NC_000014.9:26585638:ATATATATATA:ATATATATA	NC_000014.9:26585638:ATATATATATA:A… NC_000014.9:26585638:ATATATATATA:ATATATATA	(self)
ss553541361	NC_000014.7:26124684::AT	NC_000014.9:26585638:ATATATATATA:A… NC_000014.9:26585638:ATATATATATA:ATATATATATATA	(self)
ss289210020	NC_000014.7:26124695::TA	NC_000014.9:26585638:ATATATATATA:A… NC_000014.9:26585638:ATATATATATA:ATATATATATATA	(self)
63235046, 70386053, 7813215, ss500133970, ss664216715, ss1373849603, ss2925631070, ss5212416746, ss5655852446, ss5947271183	NC_000014.8:27054844::AT	NC_000014.9:26585638:ATATATATATA:A… NC_000014.9:26585638:ATATATATATA:ATATATATATATA	(self)
83055856, 30956480, 98822451, ss3817436203, ss3974578479, ss4964357092, ss5295585283, ss5489705372, ss5595529921, ss5764985347, ss5814593846, ss5900619676	NC_000014.9:26585638::AT	NC_000014.9:26585638:ATATATATATA:A… NC_000014.9:26585638:ATATATATATA:ATATATATATATA	(self)
4864515870	NC_000014.9:26585638:ATATATATATA:A… NC_000014.9:26585638:ATATATATATA:ATATATATATATA	NC_000014.9:26585638:ATATATATATA:A… NC_000014.9:26585638:ATATATATATA:ATATATATATATA	(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 rs201369181

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs201369181