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dbSNP Short Genetic Variations

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.

rs77876839

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:6273621 (GRCh38.p13) 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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.024073 (6372/264690, TOPMED)
T=0.017917 (2512/140200, GnomAD)
T=0.01154 (218/18890, ALFA) (+ 11 more)
T=0.21372 (3582/16760, 8.3KJPN)
T=0.0455 (228/5008, 1000G)
T=0.0058 (26/4480, Estonian)
T=0.0008 (3/3854, ALSPAC)
T=0.0008 (3/3708, TWINSUK)
T=0.2020 (592/2930, KOREAN)
T=0.2036 (373/1832, Korea1K)
T=0.118 (25/212, Vietnamese)
C=0.46 (23/50, SGDP_PRJ)
C=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
Help

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.p13 chr 10 NC_000010.11:g.6273621C>T
GRCh37.p13 chr 10 NC_000010.10:g.6315584C>T
Help

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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 C=0.98846 T=0.01154
European Sub 14286 C=0.99706 T=0.00294
African Sub 2946 C=0.9725 T=0.0275
African Others Sub 114 C=0.956 T=0.044
African American Sub 2832 C=0.9732 T=0.0268
Asian Sub 112 C=0.750 T=0.250
East Asian Sub 86 C=0.73 T=0.27
Other Asian Sub 26 C=0.81 T=0.19
Latin American 1 Sub 146 C=0.973 T=0.027
Latin American 2 Sub 610 C=0.933 T=0.067
South Asian Sub 98 C=0.98 T=0.02
Other Sub 692 C=0.971 T=0.029


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.975927 T=0.024073
gnomAD - Genomes Global Study-wide 140200 C=0.982083 T=0.017917
gnomAD - Genomes European Sub 75942 C=0.99816 T=0.00184
gnomAD - Genomes African Sub 42026 C=0.97352 T=0.02648
gnomAD - Genomes American Sub 13646 C=0.95427 T=0.04573
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9988 T=0.0012
gnomAD - Genomes East Asian Sub 3120 C=0.8125 T=0.1875
gnomAD - Genomes Other Sub 2144 C=0.9785 T=0.0215
8.3KJPN JAPANESE Study-wide 16760 C=0.78628 T=0.21372
1000Genomes Global Study-wide 5008 C=0.9545 T=0.0455
1000Genomes African Sub 1322 C=0.9690 T=0.0310
1000Genomes East Asian Sub 1008 C=0.8492 T=0.1508
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=0.996 T=0.004
1000Genomes American Sub 694 C=0.955 T=0.045
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9942 T=0.0058
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9992 T=0.0008
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9992 T=0.0008
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.7980 T=0.2020
Korean Genome Project KOREAN Study-wide 1832 C=0.7964 T=0.2036
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.882 T=0.118
SGDP_PRJ Global Study-wide 50 C=0.46 T=0.54
Siberian Global Study-wide 2 C=0.5 T=0.5
Help

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 C= T
GRCh38.p13 chr 10 NC_000010.11:g.6273621= NC_000010.11:g.6273621C>T
GRCh37.p13 chr 10 NC_000010.10:g.6315584= NC_000010.10:g.6315584C>T
Help

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#.

29 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 BGI ss102850387 Dec 01, 2009 (131)
2 GMI ss154522782 Dec 01, 2009 (131)
3 1000GENOMES ss224544554 Jul 14, 2010 (132)
4 1000GENOMES ss241773903 Jul 15, 2010 (132)
5 GMI ss280464770 May 04, 2012 (137)
6 TISHKOFF ss561745425 Apr 25, 2013 (138)
7 SSMP ss656251656 Apr 25, 2013 (138)
8 JMKIDD_LAB ss1076731732 Aug 21, 2014 (142)
9 1000GENOMES ss1336130242 Aug 21, 2014 (142)
10 EVA_UK10K_ALSPAC ss1623911828 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1666905861 Apr 01, 2015 (144)
12 GENOMED ss1967049558 Jul 19, 2016 (147)
13 JJLAB ss2025962272 Sep 14, 2016 (149)
14 USC_VALOUEV ss2154204308 Dec 20, 2016 (150)
15 HUMAN_LONGEVITY ss2172358743 Dec 20, 2016 (150)
16 TOPMED ss2335067847 Dec 20, 2016 (150)
17 SYSTEMSBIOZJU ss2627450041 Nov 08, 2017 (151)
18 GRF ss2698428218 Nov 08, 2017 (151)
19 GNOMAD ss2885105535 Nov 08, 2017 (151)
20 TOPMED ss3110664812 Nov 08, 2017 (151)
21 EGCUT_WGS ss3673402789 Jul 13, 2019 (153)
22 EVA_DECODE ss3689206626 Jul 13, 2019 (153)
23 EVA ss3747699709 Jul 13, 2019 (153)
24 KHV_HUMAN_GENOMES ss3813062669 Jul 13, 2019 (153)
25 SGDP_PRJ ss3873453549 Apr 26, 2020 (154)
26 KRGDB ss3921389022 Apr 26, 2020 (154)
27 KOGIC ss3967131422 Apr 26, 2020 (154)
28 TOPMED ss4841243961 Apr 26, 2021 (155)
29 TOMMO_GENOMICS ss5196096974 Apr 26, 2021 (155)
30 1000Genomes NC_000010.10 - 6315584 Oct 12, 2018 (152)
31 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 6315584 Oct 12, 2018 (152)
32 Genetic variation in the Estonian population NC_000010.10 - 6315584 Oct 12, 2018 (152)
33 gnomAD - Genomes NC_000010.11 - 6273621 Apr 26, 2021 (155)
34 KOREAN population from KRGDB NC_000010.10 - 6315584 Apr 26, 2020 (154)
35 Korean Genome Project NC_000010.11 - 6273621 Apr 26, 2020 (154)
36 SGDP_PRJ NC_000010.10 - 6315584 Apr 26, 2020 (154)
37 Siberian NC_000010.10 - 6315584 Apr 26, 2020 (154)
38 8.3KJPN NC_000010.10 - 6315584 Apr 26, 2021 (155)
39 TopMed NC_000010.11 - 6273621 Apr 26, 2021 (155)
40 UK 10K study - Twins NC_000010.10 - 6315584 Oct 12, 2018 (152)
41 A Vietnamese Genetic Variation Database NC_000010.10 - 6315584 Jul 13, 2019 (153)
42 ALFA NC_000010.11 - 6273621 Apr 26, 2021 (155)
Help

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
ss280464770 NC_000010.9:6355589:C:T NC_000010.11:6273620:C:T (self)
48471559, 26932237, 19141037, 28566416, 25470529, 6720662, 54066281, 26932237, 5978602, ss224544554, ss241773903, ss561745425, ss656251656, ss1076731732, ss1336130242, ss1623911828, ss1666905861, ss1967049558, ss2025962272, ss2154204308, ss2335067847, ss2627450041, ss2698428218, ss2885105535, ss3673402789, ss3747699709, ss3873453549, ss3921389022, ss5196096974 NC_000010.10:6315583:C:T NC_000010.11:6273620:C:T (self)
342416676, 23509423, 35684426, 56789616, 5535891450, ss2172358743, ss3110664812, ss3689206626, ss3813062669, ss3967131422, ss4841243961 NC_000010.11:6273620:C:T NC_000010.11:6273620:C:T (self)
ss102850387, ss154522782 NT_008705.16:6255583:C:T NC_000010.11:6273620:C:T (self)
Help

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

No publications for rs77876839

Help

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.

Software version is: 2.0.1.post596+ae089ad