Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs11954519

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:39902263 (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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.192603 (50980/264690, TOPMED)
T=0.204247 (28615/140100, GnomAD)
T=0.02997 (847/28258, 14KJPN) (+ 19 more)
T=0.23965 (4527/18890, ALFA)
T=0.02900 (486/16760, 8.3KJPN)
T=0.1544 (989/6404, 1000G_30x)
T=0.1516 (759/5008, 1000G)
T=0.2893 (1296/4480, Estonian)
T=0.2577 (993/3854, ALSPAC)
T=0.2767 (1026/3708, TWINSUK)
T=0.0092 (27/2922, KOREAN)
T=0.0120 (22/1832, Korea1K)
T=0.242 (242/998, GoNL)
T=0.013 (10/792, PRJEB37584)
T=0.238 (143/600, NorthernSweden)
T=0.157 (48/306, HapMap)
T=0.208 (45/216, Qatari)
T=0.009 (2/216, Vietnamese)
A=0.457 (64/140, SGDP_PRJ)
T=0.24 (10/42, Ancient Sardinia)
T=0.30 (12/40, GENOME_DK)
A=0.46 (11/24, 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 A=0.76035 T=0.23965
European Sub 14286 A=0.72911 T=0.27089
African Sub 2946 A=0.8856 T=0.1144
African Others Sub 114 A=0.912 T=0.088
African American Sub 2832 A=0.8845 T=0.1155
Asian Sub 112 A=0.955 T=0.045
East Asian Sub 86 A=0.95 T=0.05
Other Asian Sub 26 A=0.96 T=0.04
Latin American 1 Sub 146 A=0.767 T=0.233
Latin American 2 Sub 610 A=0.816 T=0.184
South Asian Sub 98 A=0.73 T=0.27
Other Sub 692 A=0.793 T=0.207


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=0.807397 T=0.192603
gnomAD - Genomes Global Study-wide 140100 A=0.795753 T=0.204247
gnomAD - Genomes European Sub 75840 A=0.73143 T=0.26857
gnomAD - Genomes African Sub 42014 A=0.89722 T=0.10278
gnomAD - Genomes American Sub 13644 A=0.79280 T=0.20720
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.8011 T=0.1989
gnomAD - Genomes East Asian Sub 3130 A=0.9936 T=0.0064
gnomAD - Genomes Other Sub 2148 A=0.8040 T=0.1960
14KJPN JAPANESE Study-wide 28258 A=0.97003 T=0.02997
Allele Frequency Aggregator Total Global 18890 A=0.76035 T=0.23965
Allele Frequency Aggregator European Sub 14286 A=0.72911 T=0.27089
Allele Frequency Aggregator African Sub 2946 A=0.8856 T=0.1144
Allele Frequency Aggregator Other Sub 692 A=0.793 T=0.207
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.816 T=0.184
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.767 T=0.233
Allele Frequency Aggregator Asian Sub 112 A=0.955 T=0.045
Allele Frequency Aggregator South Asian Sub 98 A=0.73 T=0.27
8.3KJPN JAPANESE Study-wide 16760 A=0.97100 T=0.02900
1000Genomes_30x Global Study-wide 6404 A=0.8456 T=0.1544
1000Genomes_30x African Sub 1786 A=0.9216 T=0.0784
1000Genomes_30x Europe Sub 1266 A=0.7235 T=0.2765
1000Genomes_30x South Asian Sub 1202 A=0.7704 T=0.2296
1000Genomes_30x East Asian Sub 1170 A=0.9897 T=0.0103
1000Genomes_30x American Sub 980 A=0.785 T=0.215
1000Genomes Global Study-wide 5008 A=0.8484 T=0.1516
1000Genomes African Sub 1322 A=0.9191 T=0.0809
1000Genomes East Asian Sub 1008 A=0.9901 T=0.0099
1000Genomes Europe Sub 1006 A=0.7326 T=0.2674
1000Genomes South Asian Sub 978 A=0.770 T=0.230
1000Genomes American Sub 694 A=0.787 T=0.213
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.7107 T=0.2893
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.7423 T=0.2577
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.7233 T=0.2767
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9908 T=0.0092
Korean Genome Project KOREAN Study-wide 1832 A=0.9880 T=0.0120
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.758 T=0.242
CNV burdens in cranial meningiomas Global Study-wide 792 A=0.987 T=0.013
CNV burdens in cranial meningiomas CRM Sub 792 A=0.987 T=0.013
Northern Sweden ACPOP Study-wide 600 A=0.762 T=0.238
HapMap Global Study-wide 306 A=0.843 T=0.157
HapMap African Sub 110 A=0.945 T=0.055
HapMap American Sub 110 A=0.645 T=0.355
HapMap Asian Sub 86 A=0.97 T=0.03
Qatari Global Study-wide 216 A=0.792 T=0.208
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.991 T=0.009
SGDP_PRJ Global Study-wide 140 A=0.457 T=0.543
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 42 A=0.76 T=0.24
The Danish reference pan genome Danish Study-wide 40 A=0.70 T=0.30
Siberian Global Study-wide 24 A=0.46 T=0.54
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 5 NC_000005.10:g.39902263A>T
GRCh37.p13 chr 5 NC_000005.9:g.39902365A>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
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= T
GRCh38.p14 chr 5 NC_000005.10:g.39902263= NC_000005.10:g.39902263A>T
GRCh37.p13 chr 5 NC_000005.9:g.39902365= NC_000005.9:g.39902365A>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#.

68 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss17847971 Feb 28, 2004 (120)
2 SSAHASNP ss22220447 Apr 05, 2004 (121)
3 ABI ss44602964 Mar 15, 2006 (126)
4 HUMANGENOME_JCVI ss98614154 Feb 05, 2009 (130)
5 1000GENOMES ss108979889 Jan 23, 2009 (130)
6 ENSEMBL ss143336113 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss162197395 Jul 04, 2010 (132)
8 COMPLETE_GENOMICS ss166450390 Jul 04, 2010 (132)
9 1000GENOMES ss221638790 Jul 14, 2010 (132)
10 1000GENOMES ss232915103 Jul 14, 2010 (132)
11 BL ss253393603 May 09, 2011 (134)
12 GMI ss285161300 Apr 25, 2013 (138)
13 PJP ss293573272 May 09, 2011 (134)
14 TISHKOFF ss558342527 Apr 25, 2013 (138)
15 SSMP ss652197787 Apr 25, 2013 (138)
16 EVA-GONL ss981474669 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1072564327 Aug 21, 2014 (142)
18 1000GENOMES ss1314748930 Aug 21, 2014 (142)
19 EVA_GENOME_DK ss1581104309 Apr 01, 2015 (144)
20 EVA_DECODE ss1590997523 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1612711438 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1655705471 Apr 01, 2015 (144)
23 HAMMER_LAB ss1803400208 Sep 08, 2015 (146)
24 WEILL_CORNELL_DGM ss1924736976 Feb 12, 2016 (147)
25 GENOMED ss1970070379 Jul 19, 2016 (147)
26 JJLAB ss2022971655 Sep 14, 2016 (149)
27 USC_VALOUEV ss2151122844 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2273085926 Dec 20, 2016 (150)
29 GRF ss2706661050 Nov 08, 2017 (151)
30 GNOMAD ss2823558537 Nov 08, 2017 (151)
31 SWEGEN ss2996782274 Nov 08, 2017 (151)
32 ILLUMINA ss3022483557 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3025271152 Nov 08, 2017 (151)
34 CSHL ss3346347907 Nov 08, 2017 (151)
35 URBANLAB ss3648038129 Oct 12, 2018 (152)
36 ILLUMINA ss3652977889 Oct 12, 2018 (152)
37 EGCUT_WGS ss3664677557 Jul 13, 2019 (153)
38 EVA_DECODE ss3714520621 Jul 13, 2019 (153)
39 ILLUMINA ss3726228261 Jul 13, 2019 (153)
40 ACPOP ss3732281337 Jul 13, 2019 (153)
41 EVA ss3763327119 Jul 13, 2019 (153)
42 PACBIO ss3785089419 Jul 13, 2019 (153)
43 PACBIO ss3790499185 Jul 13, 2019 (153)
44 PACBIO ss3795375630 Jul 13, 2019 (153)
45 KHV_HUMAN_GENOMES ss3806503148 Jul 13, 2019 (153)
46 EVA ss3829206579 Apr 26, 2020 (154)
47 EVA ss3838072833 Apr 26, 2020 (154)
48 EVA ss3843512224 Apr 26, 2020 (154)
49 SGDP_PRJ ss3861671396 Apr 26, 2020 (154)
50 KRGDB ss3908150406 Apr 26, 2020 (154)
51 KOGIC ss3956480208 Apr 26, 2020 (154)
52 EVA ss3984545997 Apr 26, 2021 (155)
53 EVA ss3985136948 Apr 26, 2021 (155)
54 TOPMED ss4656856979 Apr 26, 2021 (155)
55 TOMMO_GENOMICS ss5171336685 Apr 26, 2021 (155)
56 1000G_HIGH_COVERAGE ss5263632260 Oct 13, 2022 (156)
57 EVA ss5357008287 Oct 13, 2022 (156)
58 HUGCELL_USP ss5461891430 Oct 13, 2022 (156)
59 EVA ss5507989713 Oct 13, 2022 (156)
60 1000G_HIGH_COVERAGE ss5547087171 Oct 13, 2022 (156)
61 SANFORD_IMAGENETICS ss5624587569 Oct 13, 2022 (156)
62 SANFORD_IMAGENETICS ss5637628947 Oct 13, 2022 (156)
63 TOMMO_GENOMICS ss5707272296 Oct 13, 2022 (156)
64 YY_MCH ss5806210785 Oct 13, 2022 (156)
65 EVA ss5834813621 Oct 13, 2022 (156)
66 EVA ss5854779051 Oct 13, 2022 (156)
67 EVA ss5893838907 Oct 13, 2022 (156)
68 EVA ss5966047171 Oct 13, 2022 (156)
69 1000Genomes NC_000005.9 - 39902365 Oct 12, 2018 (152)
70 1000Genomes_30x NC_000005.10 - 39902263 Oct 13, 2022 (156)
71 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 39902365 Oct 12, 2018 (152)
72 Genetic variation in the Estonian population NC_000005.9 - 39902365 Oct 12, 2018 (152)
73 The Danish reference pan genome NC_000005.9 - 39902365 Apr 26, 2020 (154)
74 gnomAD - Genomes NC_000005.10 - 39902263 Apr 26, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000005.9 - 39902365 Apr 26, 2020 (154)
76 HapMap NC_000005.10 - 39902263 Apr 26, 2020 (154)
77 KOREAN population from KRGDB NC_000005.9 - 39902365 Apr 26, 2020 (154)
78 Korean Genome Project NC_000005.10 - 39902263 Apr 26, 2020 (154)
79 Northern Sweden NC_000005.9 - 39902365 Jul 13, 2019 (153)
80 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000005.9 - 39902365 Apr 26, 2021 (155)
81 CNV burdens in cranial meningiomas NC_000005.9 - 39902365 Apr 26, 2021 (155)
82 Qatari NC_000005.9 - 39902365 Apr 26, 2020 (154)
83 SGDP_PRJ NC_000005.9 - 39902365 Apr 26, 2020 (154)
84 Siberian NC_000005.9 - 39902365 Apr 26, 2020 (154)
85 8.3KJPN NC_000005.9 - 39902365 Apr 26, 2021 (155)
86 14KJPN NC_000005.10 - 39902263 Oct 13, 2022 (156)
87 TopMed NC_000005.10 - 39902263 Apr 26, 2021 (155)
88 UK 10K study - Twins NC_000005.9 - 39902365 Oct 12, 2018 (152)
89 A Vietnamese Genetic Variation Database NC_000005.9 - 39902365 Jul 13, 2019 (153)
90 ALFA NC_000005.10 - 39902263 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
ss108979889, ss162197395, ss166450390, ss253393603, ss285161300, ss293573272, ss1590997523 NC_000005.8:39938121:A:T NC_000005.10:39902262:A:T (self)
26337171, 14647354, 10415805, 7269248, 6509872, 15327800, 5566202, 362875, 95362, 6778906, 13688376, 3639198, 29305992, 14647354, 3256878, ss221638790, ss232915103, ss558342527, ss652197787, ss981474669, ss1072564327, ss1314748930, ss1581104309, ss1612711438, ss1655705471, ss1803400208, ss1924736976, ss1970070379, ss2022971655, ss2151122844, ss2706661050, ss2823558537, ss2996782274, ss3022483557, ss3346347907, ss3652977889, ss3664677557, ss3732281337, ss3763327119, ss3785089419, ss3790499185, ss3795375630, ss3829206579, ss3838072833, ss3861671396, ss3908150406, ss3984545997, ss3985136948, ss5171336685, ss5357008287, ss5507989713, ss5624587569, ss5637628947, ss5834813621, ss5966047171 NC_000005.9:39902364:A:T NC_000005.10:39902262:A:T (self)
34613106, 186044279, 2852242, 12858209, 41109400, 494234536, 2137572129, ss2273085926, ss3025271152, ss3648038129, ss3714520621, ss3726228261, ss3806503148, ss3843512224, ss3956480208, ss4656856979, ss5263632260, ss5461891430, ss5547087171, ss5707272296, ss5806210785, ss5854779051, ss5893838907 NC_000005.10:39902262:A:T NC_000005.10:39902262:A:T (self)
ss17847971, ss22220447 NT_006576.14:22354470:A:T NC_000005.10:39902262:A:T (self)
ss44602964, ss98614154, ss143336113 NT_006576.16:39892364:A:T NC_000005.10:39902262:A: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 rs11954519

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