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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.

rs952519

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99574972 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.057796 (15298/264690, TOPMED)
A=0.083834 (17705/211190, ALFA)
A=0.071277 (9989/140144, GnomAD) (+ 18 more)
A=0.04308 (722/16760, 8.3KJPN)
A=0.0517 (259/5008, 1000G)
A=0.1560 (699/4480, Estonian)
A=0.0911 (351/3854, ALSPAC)
A=0.0817 (303/3708, TWINSUK)
A=0.0335 (98/2922, KOREAN)
A=0.0533 (111/2084, HGDP_Stanford)
A=0.0472 (89/1886, HapMap)
A=0.0349 (64/1832, Korea1K)
A=0.0845 (96/1136, Daghestan)
A=0.099 (99/998, GoNL)
A=0.152 (91/600, NorthernSweden)
A=0.037 (8/216, Qatari)
A=0.046 (10/216, Vietnamese)
G=0.48 (26/54, SGDP_PRJ)
A=0.15 (6/40, GENOME_DK)
A=0.11 (4/38, Ancient Sardinia)
G=0.4 (4/10, 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 1 NC_000001.11:g.99574972G>A
GRCh37.p13 chr 1 NC_000001.10:g.100040528G>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

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 211190 G=0.916166 A=0.083834
European Sub 180980 G=0.909830 A=0.090170
African Sub 9724 G=0.9741 A=0.0259
African Others Sub 348 G=0.986 A=0.014
African American Sub 9376 G=0.9737 A=0.0263
Asian Sub 704 G=0.943 A=0.057
East Asian Sub 558 G=0.937 A=0.063
Other Asian Sub 146 G=0.966 A=0.034
Latin American 1 Sub 844 G=0.959 A=0.041
Latin American 2 Sub 6904 G=0.9670 A=0.0330
South Asian Sub 5042 G=0.9377 A=0.0623
Other Sub 6992 G=0.9261 A=0.0739


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 G=0.942204 A=0.057796
Allele Frequency Aggregator Total Global 211190 G=0.916166 A=0.083834
Allele Frequency Aggregator European Sub 180980 G=0.909830 A=0.090170
Allele Frequency Aggregator African Sub 9724 G=0.9741 A=0.0259
Allele Frequency Aggregator Other Sub 6992 G=0.9261 A=0.0739
Allele Frequency Aggregator Latin American 2 Sub 6904 G=0.9670 A=0.0330
Allele Frequency Aggregator South Asian Sub 5042 G=0.9377 A=0.0623
Allele Frequency Aggregator Latin American 1 Sub 844 G=0.959 A=0.041
Allele Frequency Aggregator Asian Sub 704 G=0.943 A=0.057
gnomAD - Genomes Global Study-wide 140144 G=0.928723 A=0.071277
gnomAD - Genomes European Sub 75904 G=0.89662 A=0.10338
gnomAD - Genomes African Sub 42000 G=0.97481 A=0.02519
gnomAD - Genomes American Sub 13640 G=0.96026 A=0.03974
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.9322 A=0.0678
gnomAD - Genomes East Asian Sub 3132 G=0.9413 A=0.0587
gnomAD - Genomes Other Sub 2150 G=0.9381 A=0.0619
8.3KJPN JAPANESE Study-wide 16760 G=0.95692 A=0.04308
1000Genomes Global Study-wide 5008 G=0.9483 A=0.0517
1000Genomes African Sub 1322 G=0.9826 A=0.0174
1000Genomes East Asian Sub 1008 G=0.9415 A=0.0585
1000Genomes Europe Sub 1006 G=0.8936 A=0.1064
1000Genomes South Asian Sub 978 G=0.957 A=0.043
1000Genomes American Sub 694 G=0.960 A=0.040
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8440 A=0.1560
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9089 A=0.0911
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9183 A=0.0817
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9665 A=0.0335
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.9467 A=0.0533
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.938 A=0.062
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.918 A=0.082
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.980 A=0.020
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.912 A=0.087
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.979 A=0.021
HGDP-CEPH-db Supplement 1 America Sub 216 G=1.000 A=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.89 A=0.11
HapMap Global Study-wide 1886 G=0.9528 A=0.0472
HapMap American Sub 768 G=0.934 A=0.066
HapMap African Sub 692 G=0.978 A=0.022
HapMap Asian Sub 250 G=0.956 A=0.044
HapMap Europe Sub 176 G=0.932 A=0.068
Korean Genome Project KOREAN Study-wide 1832 G=0.9651 A=0.0349
Genome-wide autozygosity in Daghestan Global Study-wide 1136 G=0.9155 A=0.0845
Genome-wide autozygosity in Daghestan Daghestan Sub 628 G=0.896 A=0.104
Genome-wide autozygosity in Daghestan Near_East Sub 144 G=0.972 A=0.028
Genome-wide autozygosity in Daghestan Central Asia Sub 122 G=0.959 A=0.041
Genome-wide autozygosity in Daghestan Europe Sub 108 G=0.907 A=0.093
Genome-wide autozygosity in Daghestan South Asian Sub 98 G=0.88 A=0.12
Genome-wide autozygosity in Daghestan Caucasus Sub 36 G=1.00 A=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.901 A=0.099
Northern Sweden ACPOP Study-wide 600 G=0.848 A=0.152
Qatari Global Study-wide 216 G=0.963 A=0.037
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.954 A=0.046
SGDP_PRJ Global Study-wide 54 G=0.48 A=0.52
The Danish reference pan genome Danish Study-wide 40 G=0.85 A=0.15
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 38 G=0.89 A=0.11
Siberian Global Study-wide 10 G=0.4 A=0.6
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 G= A
GRCh38.p13 chr 1 NC_000001.11:g.99574972= NC_000001.11:g.99574972G>A
GRCh37.p13 chr 1 NC_000001.10:g.100040528= NC_000001.10:g.100040528G>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#.

87 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1396604 Oct 05, 2000 (86)
2 ABI ss43828549 Mar 15, 2006 (126)
3 ILLUMINA ss67926497 Dec 01, 2006 (127)
4 ILLUMINA ss68048318 Dec 01, 2006 (127)
5 ILLUMINA ss68305574 Dec 12, 2006 (127)
6 PERLEGEN ss68775400 May 17, 2007 (127)
7 ILLUMINA ss71612970 May 17, 2007 (127)
8 ILLUMINA ss74928918 Dec 07, 2007 (129)
9 KRIBB_YJKIM ss83629059 Dec 15, 2007 (130)
10 ILLUMINA ss98268015 May 25, 2008 (130)
11 1000GENOMES ss108453507 Jan 23, 2009 (130)
12 ILLUMINA ss154498714 Dec 01, 2009 (131)
13 ILLUMINA ss159672576 Dec 01, 2009 (131)
14 ILLUMINA ss160995394 Dec 01, 2009 (131)
15 ILLUMINA ss174859055 Jul 04, 2010 (132)
16 1000GENOMES ss230656701 Jul 14, 2010 (132)
17 1000GENOMES ss238323672 Jul 15, 2010 (132)
18 ILLUMINA ss481923167 May 04, 2012 (137)
19 ILLUMINA ss481956112 May 04, 2012 (137)
20 ILLUMINA ss482914534 Sep 08, 2015 (146)
21 ILLUMINA ss485755381 May 04, 2012 (137)
22 ILLUMINA ss537607323 Sep 08, 2015 (146)
23 SSMP ss648253873 Apr 25, 2013 (138)
24 ILLUMINA ss778641499 Sep 08, 2015 (146)
25 ILLUMINA ss783323479 Sep 08, 2015 (146)
26 ILLUMINA ss784275332 Sep 08, 2015 (146)
27 ILLUMINA ss832585093 Sep 08, 2015 (146)
28 ILLUMINA ss833183301 Jul 12, 2019 (153)
29 ILLUMINA ss834099207 Sep 08, 2015 (146)
30 EVA-GONL ss975482927 Aug 21, 2014 (142)
31 JMKIDD_LAB ss1068127614 Aug 21, 2014 (142)
32 1000GENOMES ss1292107400 Aug 21, 2014 (142)
33 HAMMER_LAB ss1397255147 Sep 08, 2015 (146)
34 EVA_GENOME_DK ss1574271477 Apr 01, 2015 (144)
35 EVA_DECODE ss1584861219 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1600816778 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1643810811 Apr 01, 2015 (144)
38 EVA_SVP ss1712357138 Apr 01, 2015 (144)
39 ILLUMINA ss1751859108 Sep 08, 2015 (146)
40 HAMMER_LAB ss1794807539 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1918682531 Feb 12, 2016 (147)
42 JJLAB ss2019862738 Sep 14, 2016 (149)
43 USC_VALOUEV ss2147881447 Dec 20, 2016 (150)
44 HUMAN_LONGEVITY ss2165030602 Dec 20, 2016 (150)
45 TOPMED ss2327381405 Dec 20, 2016 (150)
46 ILLUMINA ss2632553614 Nov 08, 2017 (151)
47 GRF ss2697808781 Nov 08, 2017 (151)
48 GNOMAD ss2758637151 Nov 08, 2017 (151)
49 AFFY ss2984868466 Nov 08, 2017 (151)
50 AFFY ss2985519917 Nov 08, 2017 (151)
51 SWEGEN ss2987305599 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3023694967 Nov 08, 2017 (151)
53 TOPMED ss3084648590 Nov 08, 2017 (151)
54 CSHL ss3343595885 Nov 08, 2017 (151)
55 ILLUMINA ss3626165270 Oct 11, 2018 (152)
56 ILLUMINA ss3630587788 Oct 11, 2018 (152)
57 ILLUMINA ss3632903278 Oct 11, 2018 (152)
58 ILLUMINA ss3633598276 Oct 11, 2018 (152)
59 ILLUMINA ss3634339250 Oct 11, 2018 (152)
60 ILLUMINA ss3635291887 Oct 11, 2018 (152)
61 ILLUMINA ss3636016806 Oct 11, 2018 (152)
62 ILLUMINA ss3637042343 Oct 11, 2018 (152)
63 ILLUMINA ss3637775449 Oct 11, 2018 (152)
64 ILLUMINA ss3638905829 Oct 11, 2018 (152)
65 ILLUMINA ss3639765062 Oct 11, 2018 (152)
66 ILLUMINA ss3640046610 Oct 11, 2018 (152)
67 ILLUMINA ss3640984521 Oct 11, 2018 (152)
68 ILLUMINA ss3641278509 Oct 11, 2018 (152)
69 ILLUMINA ss3642785634 Oct 11, 2018 (152)
70 ILLUMINA ss3643818612 Oct 11, 2018 (152)
71 ILLUMINA ss3653640396 Oct 11, 2018 (152)
72 EGCUT_WGS ss3655390668 Jul 12, 2019 (153)
73 EVA_DECODE ss3687367027 Jul 12, 2019 (153)
74 ACPOP ss3727314010 Jul 12, 2019 (153)
75 ILLUMINA ss3744640219 Jul 12, 2019 (153)
76 EVA ss3746574038 Jul 12, 2019 (153)
77 ILLUMINA ss3772141456 Jul 12, 2019 (153)
78 KHV_HUMAN_GENOMES ss3799574816 Jul 12, 2019 (153)
79 EVA ss3826326526 Apr 25, 2020 (154)
80 HGDP ss3847343738 Apr 25, 2020 (154)
81 SGDP_PRJ ss3849477451 Apr 25, 2020 (154)
82 KRGDB ss3894555483 Apr 25, 2020 (154)
83 KOGIC ss3945091246 Apr 25, 2020 (154)
84 EVA ss3984814962 Apr 25, 2021 (155)
85 EVA ss4016927688 Apr 25, 2021 (155)
86 TOPMED ss4460695934 Apr 25, 2021 (155)
87 TOMMO_GENOMICS ss5145313042 Apr 25, 2021 (155)
88 1000Genomes NC_000001.10 - 100040528 Oct 11, 2018 (152)
89 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100040528 Oct 11, 2018 (152)
90 Genome-wide autozygosity in Daghestan NC_000001.9 - 99813116 Apr 25, 2020 (154)
91 Genetic variation in the Estonian population NC_000001.10 - 100040528 Oct 11, 2018 (152)
92 The Danish reference pan genome NC_000001.10 - 100040528 Apr 25, 2020 (154)
93 gnomAD - Genomes NC_000001.11 - 99574972 Apr 25, 2021 (155)
94 Genome of the Netherlands Release 5 NC_000001.10 - 100040528 Apr 25, 2020 (154)
95 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99813116 Apr 25, 2020 (154)
96 HapMap NC_000001.11 - 99574972 Apr 25, 2020 (154)
97 KOREAN population from KRGDB NC_000001.10 - 100040528 Apr 25, 2020 (154)
98 Korean Genome Project NC_000001.11 - 99574972 Apr 25, 2020 (154)
99 Northern Sweden NC_000001.10 - 100040528 Jul 12, 2019 (153)
100 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100040528 Apr 25, 2021 (155)
101 Qatari NC_000001.10 - 100040528 Apr 25, 2020 (154)
102 SGDP_PRJ NC_000001.10 - 100040528 Apr 25, 2020 (154)
103 Siberian NC_000001.10 - 100040528 Apr 25, 2020 (154)
104 8.3KJPN NC_000001.10 - 100040528 Apr 25, 2021 (155)
105 TopMed NC_000001.11 - 99574972 Apr 25, 2021 (155)
106 UK 10K study - Twins NC_000001.10 - 100040528 Oct 11, 2018 (152)
107 A Vietnamese Genetic Variation Database NC_000001.10 - 100040528 Jul 12, 2019 (153)
108 ALFA NC_000001.11 - 99574972 Apr 25, 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)
rs59260491 May 25, 2008 (130)
rs386623176 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638905829, ss3639765062, ss3643818612 NC_000001.8:99752548:G:A NC_000001.11:99574971:G:A (self)
16449, 21630, ss108453507, ss481923167, ss1397255147, ss1584861219, ss1712357138, ss3642785634, ss3847343738 NC_000001.9:99813115:G:A NC_000001.11:99574971:G:A (self)
2870966, 1583701, 1128916, 1628921, 687024, 1732877, 598875, 40889, 724461, 1494431, 397801, 3282349, 1583701, 341138, ss230656701, ss238323672, ss481956112, ss482914534, ss485755381, ss537607323, ss648253873, ss778641499, ss783323479, ss784275332, ss832585093, ss833183301, ss834099207, ss975482927, ss1068127614, ss1292107400, ss1574271477, ss1600816778, ss1643810811, ss1751859108, ss1794807539, ss1918682531, ss2019862738, ss2147881447, ss2327381405, ss2632553614, ss2697808781, ss2758637151, ss2984868466, ss2985519917, ss2987305599, ss3343595885, ss3626165270, ss3630587788, ss3632903278, ss3633598276, ss3634339250, ss3635291887, ss3636016806, ss3637042343, ss3637775449, ss3640046610, ss3640984521, ss3641278509, ss3653640396, ss3655390668, ss3727314010, ss3744640219, ss3746574038, ss3772141456, ss3826326526, ss3849477451, ss3894555483, ss3984814962, ss4016927688, ss5145313042 NC_000001.10:100040527:G:A NC_000001.11:99574971:G:A (self)
20295440, 136531, 1469247, 15306167, 24302269, 356777328, ss2165030602, ss3023694967, ss3084648590, ss3687367027, ss3799574816, ss3945091246, ss4460695934 NC_000001.11:99574971:G:A NC_000001.11:99574971:G:A (self)
ss1396604, ss43828549, ss67926497, ss68048318, ss68305574, ss68775400, ss71612970, ss74928918, ss83629059, ss98268015, ss154498714, ss159672576, ss160995394, ss174859055 NT_032977.9:70012445:G:A NC_000001.11:99574971:G: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 rs952519

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