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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.

rs2064619

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:12529903 (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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.383486 (101505/264690, TOPMED)
C=0.389835 (54513/139836, GnomAD)
T=0.49968 (14119/28256, 14KJPN) (+ 16 more)
C=0.40191 (7592/18890, ALFA)
C=0.49606 (8314/16760, 8.3KJPN)
C=0.3679 (2356/6404, 1000G_30x)
C=0.3686 (1846/5008, 1000G)
C=0.4339 (1944/4480, Estonian)
C=0.3882 (1496/3854, ALSPAC)
C=0.3943 (1462/3708, TWINSUK)
C=0.4406 (1291/2930, KOREAN)
C=0.369 (368/998, GoNL)
C=0.352 (211/600, NorthernSweden)
T=0.359 (125/348, SGDP_PRJ)
C=0.394 (130/330, HapMap)
C=0.417 (90/216, Qatari)
C=0.388 (83/214, Vietnamese)
T=0.40 (17/42, Siberian)
C=0.42 (17/40, 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 18890 T=0.59809 C=0.40191
European Sub 14286 T=0.58841 C=0.41159
African Sub 2946 T=0.6107 C=0.3893
African Others Sub 114 T=0.544 C=0.456
African American Sub 2832 T=0.6133 C=0.3867
Asian Sub 112 T=0.589 C=0.411
East Asian Sub 86 T=0.60 C=0.40
Other Asian Sub 26 T=0.54 C=0.46
Latin American 1 Sub 146 T=0.685 C=0.315
Latin American 2 Sub 610 T=0.716 C=0.284
South Asian Sub 98 T=0.70 C=0.30
Other Sub 692 T=0.608 C=0.392


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 T=0.616514 C=0.383486
gnomAD - Genomes Global Study-wide 139836 T=0.610165 C=0.389835
gnomAD - Genomes European Sub 75760 T=0.60013 C=0.39987
gnomAD - Genomes African Sub 41892 T=0.61272 C=0.38728
gnomAD - Genomes American Sub 13612 T=0.68028 C=0.31972
gnomAD - Genomes Ashkenazi Jewish Sub 3318 T=0.5726 C=0.4274
gnomAD - Genomes East Asian Sub 3102 T=0.5561 C=0.4439
gnomAD - Genomes Other Sub 2152 T=0.6059 C=0.3941
14KJPN JAPANESE Study-wide 28256 T=0.49968 C=0.50032
Allele Frequency Aggregator Total Global 18890 T=0.59809 C=0.40191
Allele Frequency Aggregator European Sub 14286 T=0.58841 C=0.41159
Allele Frequency Aggregator African Sub 2946 T=0.6107 C=0.3893
Allele Frequency Aggregator Other Sub 692 T=0.608 C=0.392
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.716 C=0.284
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.685 C=0.315
Allele Frequency Aggregator Asian Sub 112 T=0.589 C=0.411
Allele Frequency Aggregator South Asian Sub 98 T=0.70 C=0.30
8.3KJPN JAPANESE Study-wide 16760 T=0.50394 C=0.49606
1000Genomes_30x Global Study-wide 6404 T=0.6321 C=0.3679
1000Genomes_30x African Sub 1786 T=0.6209 C=0.3791
1000Genomes_30x Europe Sub 1266 T=0.6232 C=0.3768
1000Genomes_30x South Asian Sub 1202 T=0.6373 C=0.3627
1000Genomes_30x East Asian Sub 1170 T=0.5684 C=0.4316
1000Genomes_30x American Sub 980 T=0.734 C=0.266
1000Genomes Global Study-wide 5008 T=0.6314 C=0.3686
1000Genomes African Sub 1322 T=0.6293 C=0.3707
1000Genomes East Asian Sub 1008 T=0.5694 C=0.4306
1000Genomes Europe Sub 1006 T=0.6213 C=0.3787
1000Genomes South Asian Sub 978 T=0.633 C=0.367
1000Genomes American Sub 694 T=0.738 C=0.262
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.5661 C=0.4339
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.6118 C=0.3882
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.6057 C=0.3943
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.5594 A=0.0000, C=0.4406
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.631 C=0.369
Northern Sweden ACPOP Study-wide 600 T=0.648 C=0.352
SGDP_PRJ Global Study-wide 348 T=0.359 C=0.641
HapMap Global Study-wide 330 T=0.606 C=0.394
HapMap African Sub 120 T=0.650 C=0.350
HapMap American Sub 120 T=0.625 C=0.375
HapMap Asian Sub 90 T=0.52 C=0.48
Qatari Global Study-wide 216 T=0.583 C=0.417
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.612 C=0.388
Siberian Global Study-wide 42 T=0.40 C=0.60
The Danish reference pan genome Danish Study-wide 40 T=0.57 C=0.42
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.p14 chr 20 NC_000020.11:g.12529903T>A
GRCh38.p14 chr 20 NC_000020.11:g.12529903T>C
GRCh37.p13 chr 20 NC_000020.10:g.12510550T>A
GRCh37.p13 chr 20 NC_000020.10:g.12510550T>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
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 T= A C
GRCh38.p14 chr 20 NC_000020.11:g.12529903= NC_000020.11:g.12529903T>A NC_000020.11:g.12529903T>C
GRCh37.p13 chr 20 NC_000020.10:g.12510550= NC_000020.10:g.12510550T>A NC_000020.10:g.12510550T>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#.

71 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2976064 Apr 12, 2001 (94)
2 SC_SNP ss8339846 Apr 21, 2003 (114)
3 ABI ss41396344 Mar 14, 2006 (126)
4 HGSV ss78040603 Dec 06, 2007 (129)
5 BCMHGSC_JDW ss91643214 Mar 24, 2008 (129)
6 HUMANGENOME_JCVI ss96216392 Feb 06, 2009 (130)
7 BGI ss103729989 Dec 01, 2009 (131)
8 1000GENOMES ss111747147 Jan 25, 2009 (130)
9 1000GENOMES ss113103562 Jan 25, 2009 (130)
10 ENSEMBL ss138212472 Dec 01, 2009 (131)
11 GMI ss156183923 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss169123527 Jul 04, 2010 (132)
13 COMPLETE_GENOMICS ss171917715 Jul 04, 2010 (132)
14 BUSHMAN ss203835917 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss208601926 Jul 04, 2010 (132)
16 1000GENOMES ss228265499 Jul 14, 2010 (132)
17 1000GENOMES ss237769349 Jul 15, 2010 (132)
18 1000GENOMES ss243954434 Jul 15, 2010 (132)
19 GMI ss283306270 May 04, 2012 (137)
20 GMI ss287425233 Apr 25, 2013 (138)
21 PJP ss292614168 May 09, 2011 (134)
22 TISHKOFF ss566146164 Apr 25, 2013 (138)
23 SSMP ss662017948 Apr 25, 2013 (138)
24 EVA-GONL ss994556360 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1082086086 Aug 21, 2014 (142)
26 1000GENOMES ss1364128266 Aug 21, 2014 (142)
27 DDI ss1429000940 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1579443899 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1638447098 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1681441131 Apr 01, 2015 (144)
31 EVA_DECODE ss1698612703 Apr 01, 2015 (144)
32 HAMMER_LAB ss1809429726 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1938065691 Feb 12, 2016 (147)
34 GENOMED ss1969094956 Jul 19, 2016 (147)
35 JJLAB ss2029813012 Sep 14, 2016 (149)
36 USC_VALOUEV ss2158366376 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2241458878 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2629403071 Nov 08, 2017 (151)
39 GRF ss2704040398 Nov 08, 2017 (151)
40 GNOMAD ss2965609516 Nov 08, 2017 (151)
41 SWEGEN ss3017893167 Nov 08, 2017 (151)
42 BIOINF_KMB_FNS_UNIBA ss3028739811 Nov 08, 2017 (151)
43 CSHL ss3352426743 Nov 08, 2017 (151)
44 URBANLAB ss3650974604 Oct 12, 2018 (152)
45 EGCUT_WGS ss3684611537 Jul 13, 2019 (153)
46 EVA_DECODE ss3706590852 Jul 13, 2019 (153)
47 ACPOP ss3743262925 Jul 13, 2019 (153)
48 EVA ss3758441713 Jul 13, 2019 (153)
49 PACBIO ss3788603971 Jul 13, 2019 (153)
50 PACBIO ss3793503667 Jul 13, 2019 (153)
51 PACBIO ss3798390815 Jul 13, 2019 (153)
52 KHV_HUMAN_GENOMES ss3821614987 Jul 13, 2019 (153)
53 EVA ss3835596503 Apr 27, 2020 (154)
54 EVA ss3841423286 Apr 27, 2020 (154)
55 EVA ss3846931052 Apr 27, 2020 (154)
56 SGDP_PRJ ss3888765070 Apr 27, 2020 (154)
57 KRGDB ss3938956290 Apr 27, 2020 (154)
58 TOPMED ss5082827003 Apr 26, 2021 (155)
59 TOMMO_GENOMICS ss5228909718 Apr 26, 2021 (155)
60 1000G_HIGH_COVERAGE ss5308140195 Oct 13, 2022 (156)
61 EVA ss5436363316 Oct 13, 2022 (156)
62 HUGCELL_USP ss5500535939 Oct 13, 2022 (156)
63 EVA ss5512159887 Oct 13, 2022 (156)
64 1000G_HIGH_COVERAGE ss5614251775 Oct 13, 2022 (156)
65 SANFORD_IMAGENETICS ss5662896302 Oct 13, 2022 (156)
66 TOMMO_GENOMICS ss5787916725 Oct 13, 2022 (156)
67 YY_MCH ss5817829820 Oct 13, 2022 (156)
68 EVA ss5845466524 Oct 13, 2022 (156)
69 EVA ss5853075855 Oct 13, 2022 (156)
70 EVA ss5922739375 Oct 13, 2022 (156)
71 EVA ss5957800453 Oct 13, 2022 (156)
72 1000Genomes NC_000020.10 - 12510550 Oct 12, 2018 (152)
73 1000Genomes_30x NC_000020.11 - 12529903 Oct 13, 2022 (156)
74 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 12510550 Oct 12, 2018 (152)
75 Genetic variation in the Estonian population NC_000020.10 - 12510550 Oct 12, 2018 (152)
76 The Danish reference pan genome NC_000020.10 - 12510550 Apr 27, 2020 (154)
77 gnomAD - Genomes NC_000020.11 - 12529903 Apr 26, 2021 (155)
78 Genome of the Netherlands Release 5 NC_000020.10 - 12510550 Apr 27, 2020 (154)
79 HapMap NC_000020.11 - 12529903 Apr 27, 2020 (154)
80 KOREAN population from KRGDB NC_000020.10 - 12510550 Apr 27, 2020 (154)
81 Northern Sweden NC_000020.10 - 12510550 Jul 13, 2019 (153)
82 Qatari NC_000020.10 - 12510550 Apr 27, 2020 (154)
83 SGDP_PRJ NC_000020.10 - 12510550 Apr 27, 2020 (154)
84 Siberian NC_000020.10 - 12510550 Apr 27, 2020 (154)
85 8.3KJPN NC_000020.10 - 12510550 Apr 26, 2021 (155)
86 14KJPN NC_000020.11 - 12529903 Oct 13, 2022 (156)
87 TopMed NC_000020.11 - 12529903 Apr 26, 2021 (155)
88 UK 10K study - Twins NC_000020.10 - 12510550 Oct 12, 2018 (152)
89 A Vietnamese Genetic Variation Database NC_000020.10 - 12510550 Jul 13, 2019 (153)
90 ALFA NC_000020.11 - 12529903 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
46133684, ss3938956290 NC_000020.10:12510549:T:A NC_000020.11:12529902:T:A (self)
ss78040603, ss91643214, ss111747147, ss113103562, ss169123527, ss171917715, ss203835917, ss208601926, ss283306270, ss287425233, ss292614168, ss1698612703 NC_000020.9:12458549:T:C NC_000020.11:12529902:T:C (self)
77570181, 42943081, 30349785, 5608838, 19134234, 46133684, 16547790, 20107613, 40782050, 10882730, 86879025, 42943081, 9480901, ss228265499, ss237769349, ss243954434, ss566146164, ss662017948, ss994556360, ss1082086086, ss1364128266, ss1429000940, ss1579443899, ss1638447098, ss1681441131, ss1809429726, ss1938065691, ss1969094956, ss2029813012, ss2158366376, ss2629403071, ss2704040398, ss2965609516, ss3017893167, ss3352426743, ss3684611537, ss3743262925, ss3758441713, ss3788603971, ss3793503667, ss3798390815, ss3835596503, ss3841423286, ss3888765070, ss3938956290, ss5228909718, ss5436363316, ss5512159887, ss5662896302, ss5845466524, ss5957800453 NC_000020.10:12510549:T:C NC_000020.11:12529902:T:C (self)
101777710, 546939970, 2075844, 121753829, 357935948, 5599072824, ss2241458878, ss3028739811, ss3650974604, ss3706590852, ss3821614987, ss3846931052, ss5082827003, ss5308140195, ss5500535939, ss5614251775, ss5787916725, ss5817829820, ss5853075855, ss5922739375 NC_000020.11:12529902:T:C NC_000020.11:12529902:T:C (self)
ss2976064, ss8339846, ss41396344, ss96216392, ss103729989, ss138212472, ss156183923 NT_011387.8:12450549:T:C NC_000020.11:12529902:T: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 rs2064619

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.post761+d5e8e07