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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.

rs2379072

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:80759 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.216540 (57316/264690, TOPMED)
A=0.211619 (29652/140120, GnomAD)
A=0.16030 (3028/18890, ALFA) (+ 13 more)
A=0.07655 (1283/16760, 8.3KJPN)
A=0.2137 (1070/5008, 1000G)
A=0.1020 (393/3854, ALSPAC)
A=0.1003 (372/3708, TWINSUK)
A=0.1126 (330/2930, KOREAN)
A=0.112 (112/998, GoNL)
A=0.082 (49/600, NorthernSweden)
A=0.051 (27/534, MGP)
A=0.125 (27/216, Qatari)
A=0.192 (41/214, Vietnamese)
C=0.349 (58/166, SGDP_PRJ)
A=0.23 (9/40, GENOME_DK)
C=0.4 (4/10, Siberian)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 C=0.83970 A=0.16030
European Sub 14286 C=0.90067 A=0.09933
African Sub 2946 C=0.5346 A=0.4654
African Others Sub 114 C=0.561 A=0.439
African American Sub 2832 C=0.5335 A=0.4665
Asian Sub 112 C=0.920 A=0.080
East Asian Sub 86 C=0.93 A=0.07
Other Asian Sub 26 C=0.88 A=0.12
Latin American 1 Sub 146 C=0.863 A=0.137
Latin American 2 Sub 610 C=0.880 A=0.120
South Asian Sub 98 C=0.91 A=0.09
Other Sub 692 C=0.816 A=0.184


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=0.783460 A=0.216540
gnomAD - Genomes Global Study-wide 140120 C=0.788381 A=0.211619
gnomAD - Genomes European Sub 75910 C=0.90005 A=0.09995
gnomAD - Genomes African Sub 41952 C=0.54179 A=0.45821
gnomAD - Genomes American Sub 13660 C=0.86523 A=0.13477
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9359 A=0.0641
gnomAD - Genomes East Asian Sub 3130 C=0.8732 A=0.1268
gnomAD - Genomes Other Sub 2146 C=0.8178 A=0.1822
8.3KJPN JAPANESE Study-wide 16760 C=0.92345 A=0.07655
1000Genomes Global Study-wide 5008 C=0.7863 A=0.2137
1000Genomes African Sub 1322 C=0.4834 A=0.5166
1000Genomes East Asian Sub 1008 C=0.8879 A=0.1121
1000Genomes Europe Sub 1006 C=0.9115 A=0.0885
1000Genomes South Asian Sub 978 C=0.929 A=0.071
1000Genomes American Sub 694 C=0.833 A=0.167
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8980 A=0.1020
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8997 A=0.1003
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.8874 A=0.1126
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.888 A=0.112
Northern Sweden ACPOP Study-wide 600 C=0.918 A=0.082
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.949 A=0.051
Qatari Global Study-wide 216 C=0.875 A=0.125
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.808 A=0.192
SGDP_PRJ Global Study-wide 166 C=0.349 A=0.651
The Danish reference pan genome Danish Study-wide 40 C=0.78 A=0.23
Siberian Global Study-wide 10 C=0.4 A=0.6
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.80759C>A
GRCh37.p13 chr 10 NC_000010.10:g.126699C>A
IL9RP2 pseudogene NG_009864.2:g.5587G>T
TUBB8 RefSeqGene NG_046777.1:g.697G>T
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.70759C>A
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
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= A
GRCh38.p13 chr 10 NC_000010.11:g.80759= NC_000010.11:g.80759C>A
GRCh37.p13 chr 10 NC_000010.10:g.126699= NC_000010.10:g.126699C>A
IL9RP2 pseudogene NG_009864.2:g.5587= NG_009864.2:g.5587G>T
TUBB8 RefSeqGene NG_046777.1:g.697= NG_046777.1:g.697G>T
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.70759= NW_003571043.1:g.70759C>A
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#.

51 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3338843 Sep 28, 2001 (100)
2 SC_JCM ss4249095 Nov 05, 2001 (101)
3 SC_SNP ss12973097 Dec 05, 2003 (119)
4 SC_SNP ss16089675 Feb 27, 2004 (120)
5 SSAHASNP ss20665474 Apr 05, 2004 (121)
6 HGSV ss85120199 Dec 15, 2007 (130)
7 1000GENOMES ss115221464 Jan 25, 2009 (130)
8 ILLUMINA-UK ss118963227 Feb 15, 2009 (130)
9 ENSEMBL ss138806202 Dec 01, 2009 (131)
10 GMI ss158077330 Dec 01, 2009 (131)
11 BUSHMAN ss201023278 Jul 04, 2010 (132)
12 BCM-HGSC-SUB ss207453072 Jul 04, 2010 (132)
13 1000GENOMES ss224512347 Jul 14, 2010 (132)
14 1000GENOMES ss235012247 Jul 15, 2010 (132)
15 1000GENOMES ss241753209 Jul 15, 2010 (132)
16 GMI ss280440370 May 04, 2012 (137)
17 PJP ss290815785 May 09, 2011 (134)
18 TISHKOFF ss561707909 Apr 25, 2013 (138)
19 SSMP ss656208239 Apr 25, 2013 (138)
20 EVA-GONL ss987096718 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1076687380 Aug 21, 2014 (142)
22 1000GENOMES ss1335912675 Aug 21, 2014 (142)
23 EVA_GENOME_DK ss1574842072 Apr 09, 2015 (144)
24 EVA_DECODE ss1596744216 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1623797509 Apr 09, 2015 (144)
26 EVA_UK10K_TWINSUK ss1666791542 Apr 09, 2015 (144)
27 EVA_MGP ss1711245164 Apr 09, 2015 (144)
28 HAMMER_LAB ss1806212537 Sep 11, 2015 (146)
29 WEILL_CORNELL_DGM ss1930414702 Feb 17, 2016 (147)
30 GENOMED ss1967034964 Sep 28, 2016 (149)
31 JJLAB ss2025929540 Sep 28, 2016 (149)
32 USC_VALOUEV ss2154169597 Oct 12, 2018 (152)
33 TOPMED ss2334634872 Oct 12, 2018 (152)
34 SYSTEMSBIOZJU ss2627432615 Oct 12, 2018 (152)
35 GRF ss2698388991 Oct 12, 2018 (152)
36 GNOMAD ss2884518482 Oct 12, 2018 (152)
37 SWEGEN ss3005784284 Oct 12, 2018 (152)
38 BIOINF_KMB_FNS_UNIBA ss3026746698 Nov 08, 2017 (151)
39 TOPMED ss3109330884 Nov 08, 2017 (151)
40 OMUKHERJEE_ADBS ss3646401706 Oct 12, 2018 (152)
41 URBANLAB ss3649265485 Oct 12, 2018 (152)
42 EVA_DECODE ss3689095248 Jul 13, 2019 (153)
43 ACPOP ss3736974262 Jul 13, 2019 (153)
44 EVA ss3747627280 Jul 13, 2019 (153)
45 KHV_HUMAN_GENOMES ss3812993268 Jul 13, 2019 (153)
46 EVA ss3831916717 Apr 26, 2020 (154)
47 SGDP_PRJ ss3873326332 Apr 26, 2020 (154)
48 KRGDB ss3921253306 Apr 26, 2020 (154)
49 GNOMAD ss4211409142 Apr 26, 2021 (155)
50 TOPMED ss4839522145 Apr 26, 2021 (155)
51 TOMMO_GENOMICS ss5195847839 Apr 26, 2021 (155)
52 1000Genomes NC_000010.10 - 126699 Oct 12, 2018 (152)
53 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 126699 Oct 12, 2018 (152)
54 The Danish reference pan genome NC_000010.10 - 126699 Apr 26, 2020 (154)
55 gnomAD - Genomes NC_000010.11 - 80759 Apr 26, 2021 (155)
56 Genome of the Netherlands Release 5 NC_000010.10 - 126699 Apr 26, 2020 (154)
57 KOREAN population from KRGDB NC_000010.10 - 126699 Apr 26, 2020 (154)
58 Medical Genome Project healthy controls from Spanish population NC_000010.10 - 126699 Apr 26, 2020 (154)
59 Northern Sweden NC_000010.10 - 126699 Jul 13, 2019 (153)
60 Qatari NC_000010.10 - 126699 Apr 26, 2020 (154)
61 SGDP_PRJ NC_000010.10 - 126699 Apr 26, 2020 (154)
62 Siberian NC_000010.10 - 126699 Apr 26, 2020 (154)
63 8.3KJPN NC_000010.10 - 126699 Apr 26, 2021 (155)
64 TopMed NC_000010.11 - 80759 Apr 26, 2021 (155)
65 UK 10K study - Twins NC_000010.10 - 126699 Oct 12, 2018 (152)
66 A Vietnamese Genetic Variation Database NC_000010.10 - 126699 Jul 13, 2019 (153)
67 ALFA NC_000010.11 - 80759 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).

Associated ID History Updated (Build)
rs60709366 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85120199 NC_000010.8:116698:C:A NC_000010.11:80758:C:A (self)
ss115221464, ss118963227, ss201023278, ss207453072, ss280440370, ss290815785, ss1596744216 NC_000010.9:116698:C:A NC_000010.11:80758:C:A (self)
48246372, 26806279, 1988096, 11953845, 28430700, 360924, 10259127, 12456632, 25343312, 6685951, 53817146, 26806279, 5948657, ss224512347, ss235012247, ss241753209, ss561707909, ss656208239, ss987096718, ss1076687380, ss1335912675, ss1574842072, ss1623797509, ss1666791542, ss1711245164, ss1806212537, ss1930414702, ss1967034964, ss2025929540, ss2154169597, ss2334634872, ss2627432615, ss2698388991, ss2884518482, ss3005784284, ss3646401706, ss3736974262, ss3747627280, ss3831916717, ss3873326332, ss3921253306, ss5195847839 NC_000010.10:126698:C:A NC_000010.11:80758:C:A (self)
340932320, 34601410, 55067800, 10181004156, ss3026746698, ss3109330884, ss3649265485, ss3689095248, ss3812993268, ss4211409142, ss4839522145 NC_000010.11:80758:C:A NC_000010.11:80758:C:A (self)
ss3338843, ss4249095, ss138806202, ss158077330 NT_008705.16:66698:C:A NC_000010.11:80758:C:A (self)
ss12973097 NT_024115.14:66698:C:A NC_000010.11:80758:C:A (self)
ss16089675, ss20665474 NT_077567.3:66698:C:A NC_000010.11:80758:C:A (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 rs2379072

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.post629+eb05767