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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.

rs2379069

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:79294 (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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.139835 (37013/264690, TOPMED)
C=0.127376 (17800/139744, GnomAD)
C=0.08745 (1652/18890, ALFA) (+ 14 more)
C=0.05173 (867/16760, 8.3KJPN)
C=0.1476 (739/5008, 1000G)
C=0.0317 (122/3854, ALSPAC)
C=0.0283 (105/3708, TWINSUK)
C=0.0662 (194/2930, KOREAN)
C=0.0524 (96/1832, Korea1K)
C=0.035 (35/998, GoNL)
C=0.022 (13/600, NorthernSweden)
C=0.083 (18/216, Qatari)
C=0.130 (28/216, Vietnamese)
A=0.402 (49/122, SGDP_PRJ)
C=0.07 (3/40, GENOME_DK)
A=0.5 (5/10, Siberian)
C=0.5 (5/10, 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.79294A>C
GRCh37.p13 chr 10 NC_000010.10:g.125234A>C
TUBB8 RefSeqGene NG_046777.1:g.2162T>G
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.69294A>C
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 A=0.91255 C=0.08745
European Sub 14286 A=0.96864 C=0.03136
African Sub 2946 A=0.6422 C=0.3578
African Others Sub 114 A=0.649 C=0.351
African American Sub 2832 A=0.6419 C=0.3581
Asian Sub 112 A=0.973 C=0.027
East Asian Sub 86 A=0.97 C=0.03
Other Asian Sub 26 A=1.00 C=0.00
Latin American 1 Sub 146 A=0.904 C=0.096
Latin American 2 Sub 610 A=0.928 C=0.072
South Asian Sub 98 A=0.98 C=0.02
Other Sub 692 A=0.874 C=0.126


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 A=0.860165 C=0.139835
gnomAD - Genomes Global Study-wide 139744 A=0.872624 C=0.127376
gnomAD - Genomes European Sub 75960 A=0.97206 C=0.02794
gnomAD - Genomes African Sub 41534 A=0.66230 C=0.33770
gnomAD - Genomes American Sub 13648 A=0.92050 C=0.07950
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.9630 C=0.0370
gnomAD - Genomes East Asian Sub 3132 A=0.9345 C=0.0655
gnomAD - Genomes Other Sub 2150 A=0.8888 C=0.1112
8.3KJPN JAPANESE Study-wide 16760 A=0.94827 C=0.05173
1000Genomes Global Study-wide 5008 A=0.8524 C=0.1476
1000Genomes African Sub 1322 A=0.5893 C=0.4107
1000Genomes East Asian Sub 1008 A=0.9375 C=0.0625
1000Genomes Europe Sub 1006 A=0.9732 C=0.0268
1000Genomes South Asian Sub 978 A=0.972 C=0.028
1000Genomes American Sub 694 A=0.886 C=0.114
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9683 C=0.0317
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9717 C=0.0283
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.9338 C=0.0662
Korean Genome Project KOREAN Study-wide 1832 A=0.9476 C=0.0524
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.965 C=0.035
Northern Sweden ACPOP Study-wide 600 A=0.978 C=0.022
Qatari Global Study-wide 216 A=0.917 C=0.083
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.870 C=0.130
SGDP_PRJ Global Study-wide 122 A=0.402 C=0.598
The Danish reference pan genome Danish Study-wide 40 A=0.93 C=0.07
Siberian Global Study-wide 10 A=0.5 C=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 A= C
GRCh38.p13 chr 10 NC_000010.11:g.79294= NC_000010.11:g.79294A>C
GRCh37.p13 chr 10 NC_000010.10:g.125234= NC_000010.10:g.125234A>C
TUBB8 RefSeqGene NG_046777.1:g.2162= NG_046777.1:g.2162T>G
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.69294= NW_003571043.1:g.69294A>C
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#.

43 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3338840 Sep 28, 2001 (100)
2 SC_SNP ss12973420 Dec 05, 2003 (119)
3 SC_SNP ss16089668 Feb 27, 2004 (120)
4 PERLEGEN ss23227511 Sep 20, 2004 (124)
5 ILLUMINA-UK ss118963210 Feb 15, 2009 (131)
6 GMI ss158077299 Dec 01, 2009 (131)
7 BUSHMAN ss201023256 Jul 04, 2010 (132)
8 BCM-HGSC-SUB ss207375064 Jul 04, 2010 (132)
9 1000GENOMES ss210876160 Jul 14, 2010 (132)
10 1000GENOMES ss224512326 Jul 14, 2010 (132)
11 1000GENOMES ss235012226 Jul 15, 2010 (132)
12 1000GENOMES ss241753203 Jul 15, 2010 (132)
13 GMI ss280440365 May 04, 2012 (137)
14 PJP ss290815782 May 09, 2011 (134)
15 TISHKOFF ss561707904 Apr 25, 2013 (138)
16 SSMP ss656208231 Apr 25, 2013 (138)
17 EVA-GONL ss987096710 Aug 21, 2014 (142)
18 1000GENOMES ss1335912632 Aug 21, 2014 (142)
19 EVA_GENOME_DK ss1574842066 Apr 09, 2015 (144)
20 EVA_DECODE ss1596744208 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1623797486 Apr 09, 2015 (144)
22 EVA_UK10K_TWINSUK ss1666791519 Apr 09, 2015 (144)
23 WEILL_CORNELL_DGM ss1930414693 Feb 17, 2016 (147)
24 GENOMED ss1967034961 Sep 28, 2016 (149)
25 JJLAB ss2025929536 Sep 28, 2016 (149)
26 USC_VALOUEV ss2154169590 Oct 12, 2018 (152)
27 TOPMED ss2334634790 Oct 12, 2018 (152)
28 SYSTEMSBIOZJU ss2627432609 Oct 12, 2018 (152)
29 GRF ss2698388985 Oct 12, 2018 (152)
30 GNOMAD ss2884518313 Oct 12, 2018 (152)
31 SWEGEN ss3005784262 Oct 12, 2018 (152)
32 TOPMED ss3109330616 Nov 08, 2017 (151)
33 EVA_DECODE ss3689095232 Jul 13, 2019 (153)
34 ACPOP ss3736974257 Jul 13, 2019 (153)
35 EVA ss3747627267 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3812993253 Jul 13, 2019 (153)
37 EVA ss3831916712 Apr 26, 2020 (154)
38 SGDP_PRJ ss3873326311 Apr 26, 2020 (154)
39 KRGDB ss3921253291 Apr 26, 2020 (154)
40 KOGIC ss3967022698 Apr 26, 2020 (154)
41 GNOMAD ss4211408836 Apr 26, 2021 (155)
42 TOPMED ss4839521810 Apr 26, 2021 (155)
43 TOMMO_GENOMICS ss5195847793 Apr 26, 2021 (155)
44 1000Genomes NC_000010.10 - 125234 Oct 12, 2018 (152)
45 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 125234 Oct 12, 2018 (152)
46 The Danish reference pan genome NC_000010.10 - 125234 Apr 26, 2020 (154)
47 gnomAD - Genomes NC_000010.11 - 79294 Apr 26, 2021 (155)
48 Genome of the Netherlands Release 5 NC_000010.10 - 125234 Apr 26, 2020 (154)
49 KOREAN population from KRGDB NC_000010.10 - 125234 Apr 26, 2020 (154)
50 Korean Genome Project NC_000010.11 - 79294 Apr 26, 2020 (154)
51 Northern Sweden NC_000010.10 - 125234 Jul 13, 2019 (153)
52 Qatari NC_000010.10 - 125234 Apr 26, 2020 (154)
53 SGDP_PRJ NC_000010.10 - 125234 Apr 26, 2020 (154)
54 Siberian NC_000010.10 - 125234 Apr 26, 2020 (154)
55 8.3KJPN NC_000010.10 - 125234 Apr 26, 2021 (155)
56 TopMed NC_000010.11 - 79294 Apr 26, 2021 (155)
57 UK 10K study - Twins NC_000010.10 - 125234 Oct 12, 2018 (152)
58 A Vietnamese Genetic Variation Database NC_000010.10 - 125234 Jul 13, 2019 (153)
59 ALFA NC_000010.11 - 79294 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)
rs17277541 Dec 02, 2004 (124)
rs74113797 Dec 02, 2009 (131)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss118963210, ss201023256, ss207375064, ss210876160, ss280440365, ss290815782, ss1596744208 NC_000010.9:115233:A:C NC_000010.11:79293:A:C (self)
48246328, 26806256, 1988094, 11953837, 28430685, 10259122, 12456623, 25343291, 6685944, 53817100, 26806256, 5948651, ss224512326, ss235012226, ss241753203, ss561707904, ss656208231, ss987096710, ss1335912632, ss1574842066, ss1623797486, ss1666791519, ss1930414693, ss1967034961, ss2025929536, ss2154169590, ss2334634790, ss2627432609, ss2698388985, ss2884518313, ss3005784262, ss3736974257, ss3747627267, ss3831916712, ss3873326311, ss3921253291, ss5195847793 NC_000010.10:125233:A:C NC_000010.11:79293:A:C (self)
340932011, 23400699, 34601195, 55067465, 3457974887, ss3109330616, ss3689095232, ss3812993253, ss3967022698, ss4211408836, ss4839521810 NC_000010.11:79293:A:C NC_000010.11:79293:A:C (self)
ss3338840, ss23227511, ss158077299 NT_008705.16:65233:A:C NC_000010.11:79293:A:C (self)
ss12973420 NT_024115.14:65233:A:C NC_000010.11:79293:A:C (self)
ss16089668 NT_077567.3:65233:A:C NC_000010.11:79293:A:C (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 rs2379069

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