Name: rs4769981
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.

rs4769981

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:18624422 (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: G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.006902 (1827/264690, TOPMED)
G=0.006111 (855/139902, GnomAD)
G=0.00000 (0/28258, 14KJPN) (+ 11 more)
G=0.00319 (59/18520, ALFA)
G=0.00000 (0/16760, 8.3KJPN)
G=0.0055 (35/6404, 1000G_30x)
G=0.0054 (27/5008, 1000G)
G=0.0003 (1/2926, KOREAN)
G=0.0000 (0/1832, Korea1K)
G=0.001 (1/998, GoNL)
G=0.000 (0/600, NorthernSweden)
G=0.004 (2/558, SGDP_PRJ)
G=0.000 (0/216, Qatari)
G=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18520	G=0.00319	C=0.99681
European	Sub	14152	G=0.00035	C=0.99965
African	Sub	2898	G=0.0162	C=0.9838
African Others	Sub	114	G=0.026	C=0.974
African American	Sub	2784	G=0.0158	C=0.9842
Asian	Sub	112	G=0.000	C=1.000
East Asian	Sub	86	G=0.00	C=1.00
Other Asian	Sub	26	G=0.00	C=1.00
Latin American 1	Sub	146	G=0.000	C=1.000
Latin American 2	Sub	610	G=0.003	C=0.997
South Asian	Sub	98	G=0.00	C=1.00
Other	Sub	504	G=0.010	C=0.990

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
TopMed	Global	Study-wide	264690	G=0.006902	C=0.993098
gnomAD - Genomes	Global	Study-wide	139902	G=0.006111	C=0.993889
gnomAD - Genomes	European	Sub	75828	G=0.00038	C=0.99962
gnomAD - Genomes	African	Sub	41890	G=0.01721	C=0.98279
gnomAD - Genomes	American	Sub	13608	G=0.00625	C=0.99375
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.0024	C=0.9976
gnomAD - Genomes	East Asian	Sub	3128	G=0.0000	C=1.0000
gnomAD - Genomes	Other	Sub	2130	G=0.0056	C=0.9944
14KJPN	JAPANESE	Study-wide	28258	G=0.00000	C=1.00000
Allele Frequency Aggregator	Total	Global	18520	G=0.00319	C=0.99681
Allele Frequency Aggregator	European	Sub	14152	G=0.00035	C=0.99965
Allele Frequency Aggregator	African	Sub	2898	G=0.0162	C=0.9838
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.003	C=0.997
Allele Frequency Aggregator	Other	Sub	504	G=0.010	C=0.990
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.000	C=1.000
Allele Frequency Aggregator	Asian	Sub	112	G=0.000	C=1.000
Allele Frequency Aggregator	South Asian	Sub	98	G=0.00	C=1.00
8.3KJPN	JAPANESE	Study-wide	16760	G=0.00000	C=1.00000
1000Genomes_30x	Global	Study-wide	6404	G=0.0055	C=0.9945
1000Genomes_30x	African	Sub	1786	G=0.0179	C=0.9821
1000Genomes_30x	Europe	Sub	1266	G=0.0016	C=0.9984
1000Genomes_30x	South Asian	Sub	1202	G=0.0000	C=1.0000
1000Genomes_30x	East Asian	Sub	1170	G=0.0000	C=1.0000
1000Genomes_30x	American	Sub	980	G=0.001	C=0.999
1000Genomes	Global	Study-wide	5008	G=0.0054	C=0.9946
1000Genomes	African	Sub	1322	G=0.0189	C=0.9811
1000Genomes	East Asian	Sub	1008	G=0.0000	C=1.0000
1000Genomes	Europe	Sub	1006	G=0.0010	C=0.9990
1000Genomes	South Asian	Sub	978	G=0.000	C=1.000
1000Genomes	American	Sub	694	G=0.001	C=0.999
KOREAN population from KRGDB	KOREAN	Study-wide	2926	G=0.0003	C=0.9997, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	G=0.0000	C=1.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.001	C=0.999
Northern Sweden	ACPOP	Study-wide	600	G=0.000	C=1.000
SGDP_PRJ	Global	Study-wide	558	G=0.004	C=0.996
Qatari	Global	Study-wide	216	G=0.000	C=1.000
The Danish reference pan genome	Danish	Study-wide	40	G=0.00	C=1.00

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 13	NC_000013.11:g.18624422G>C
GRCh38.p14 chr 13	NC_000013.11:g.18624422G>T
GRCh37.p13 chr 13	NC_000013.10:g.19198562G>C
GRCh37.p13 chr 13	NC_000013.10:g.19198562G>T

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	G=	C	T
GRCh38.p14 chr 13	NC_000013.11:g.18624422=	NC_000013.11:g.18624422G>C	NC_000013.11:g.18624422G>T
GRCh37.p13 chr 13	NC_000013.10:g.19198562=	NC_000013.10:g.19198562G>C	NC_000013.10:g.19198562G>T

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#.

45 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6580170	Feb 20, 2003 (111)
2	SC_SNP	ss13257492	Dec 05, 2003 (119)
3	ABI	ss40406865	Mar 14, 2006 (126)
4	HGSV	ss81233624	Dec 16, 2007 (130)
5	BCMHGSC_JDW	ss89496648	Mar 24, 2008 (129)
6	HUMANGENOME_JCVI	ss96946431	Feb 06, 2009 (130)
7	ILLUMINA-UK	ss118370076	Feb 14, 2009 (130)
8	ENSEMBL	ss143516297	Dec 01, 2009 (131)
9	BCM-HGSC-SUB	ss206808848	Jul 04, 2010 (132)
10	BL	ss254804252	May 09, 2011 (134)
11	GMI	ss281616415	May 04, 2012 (137)
12	1000GENOMES	ss337729012	May 09, 2011 (134)
13	SSMP	ss659107435	Apr 25, 2013 (138)
14	EVA-GONL	ss990138599	Aug 21, 2014 (142)
15	1000GENOMES	ss1347311425	Aug 21, 2014 (142)
16	DDI	ss1427109283	Apr 01, 2015 (144)
17	EVA_GENOME_DK	ss1576632942	Apr 01, 2015 (144)
18	WEILL_CORNELL_DGM	ss1933503786	Feb 12, 2016 (147)
19	GRF	ss2700235514	Nov 08, 2017 (151)
20	GNOMAD	ss2917081436	Nov 08, 2017 (151)
21	SWEGEN	ss3010634474	Nov 08, 2017 (151)
22	CSHL	ss3350336313	Nov 08, 2017 (151)
23	URBANLAB	ss3649972874	Oct 12, 2018 (152)
24	EVA_DECODE	ss3694827865	Jul 13, 2019 (153)
25	ACPOP	ss3739535854	Jul 13, 2019 (153)
26	PACBIO	ss3787387482	Jul 13, 2019 (153)
27	PACBIO	ss3792463257	Jul 13, 2019 (153)
28	PACBIO	ss3797346841	Jul 13, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3816505110	Jul 13, 2019 (153)
30	EVA	ss3833419837	Apr 27, 2020 (154)
31	EVA	ss3840283375	Apr 27, 2020 (154)
32	EVA	ss3845767325	Apr 27, 2020 (154)
33	SGDP_PRJ	ss3879488906	Apr 27, 2020 (154)
34	KRGDB	ss3928294035	Apr 27, 2020 (154)
35	KOGIC	ss3973115618	Apr 27, 2020 (154)
36	TOPMED	ss4938438364	Apr 26, 2021 (155)
37	TOMMO_GENOMICS	ss5208966194	Apr 26, 2021 (155)
38	1000G_HIGH_COVERAGE	ss5292927793	Oct 16, 2022 (156)
39	EVA	ss5409325625	Oct 16, 2022 (156)
40	1000G_HIGH_COVERAGE	ss5591488048	Oct 16, 2022 (156)
41	SANFORD_IMAGENETICS	ss5654300667	Oct 16, 2022 (156)
42	TOMMO_GENOMICS	ss5760545469	Oct 16, 2022 (156)
43	YY_MCH	ss5813903179	Oct 16, 2022 (156)
44	EVA	ss5839150610	Oct 16, 2022 (156)
45	EVA	ss5945710480	Oct 16, 2022 (156)
46	1000Genomes	NC_000013.10 - 19198562	Oct 12, 2018 (152)
47	1000Genomes_30x	NC_000013.11 - 18624422	Oct 16, 2022 (156)
48	The Danish reference pan genome	NC_000013.10 - 19198562	Apr 27, 2020 (154)
49	gnomAD - Genomes	NC_000013.11 - 18624422	Apr 26, 2021 (155)
50	Genome of the Netherlands Release 5	NC_000013.10 - 19198562	Apr 27, 2020 (154)
51	KOREAN population from KRGDB	NC_000013.10 - 19198562	Apr 27, 2020 (154)
52	Korean Genome Project	NC_000013.11 - 18624422	Apr 27, 2020 (154)
53	Northern Sweden	NC_000013.10 - 19198562	Jul 13, 2019 (153)
54	Qatari	NC_000013.10 - 19198562	Apr 27, 2020 (154)
55	SGDP_PRJ	NC_000013.10 - 19198562	Apr 27, 2020 (154)
56	8.3KJPN	NC_000013.10 - 19198562	Apr 26, 2021 (155)
57	14KJPN	NC_000013.11 - 18624422	Oct 16, 2022 (156)
58	TopMed	NC_000013.11 - 18624422	Apr 26, 2021 (155)
59	ALFA	NC_000013.11 - 18624422	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)
rs61203662	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss81233624, ss89496648, ss118370076, ss206808848, ss254804252, ss281616415	NC_000013.9:18096561:G:C	NC_000013.11:18624421:G:C	(self)
60147257, 3197415, 14898459, 35471429, 12820719, 15545716, 31505886, 66935501, ss337729012, ss659107435, ss990138599, ss1347311425, ss1427109283, ss1576632942, ss1933503786, ss2700235514, ss2917081436, ss3010634474, ss3350336313, ss3739535854, ss3787387482, ss3792463257, ss3797346841, ss3833419837, ss3840283375, ss3879488906, ss3928294035, ss5208966194, ss5409325625, ss5654300667, ss5839150610, ss5945710480	NC_000013.10:19198561:G:C	NC_000013.11:18624421:G:C	(self)
79013983, 424233360, 29493619, 94382573, 153984022, 16606176082, ss3649972874, ss3694827865, ss3816505110, ss3845767325, ss3973115618, ss4938438364, ss5292927793, ss5591488048, ss5760545469, ss5813903179	NC_000013.11:18624421:G:C	NC_000013.11:18624421:G:C	(self)
ss13257492	NT_009799.12:178561:G:C	NC_000013.11:18624421:G:C	(self)
ss6580170, ss40406865, ss96946431, ss143516297	NT_024524.14:178561:G:C	NC_000013.11:18624421:G:C	(self)
35471429, ss3928294035	NC_000013.10:19198561:G:T	NC_000013.11:18624421:G:T	(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 rs4769981

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

rs4769981