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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.

rs10003241

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:153428862 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.193910 (51326/264690, TOPMED)
A=0.186562 (26137/140098, GnomAD)
A=0.16224 (11000/67802, ALFA) (+ 17 more)
A=0.18858 (5329/28258, 14KJPN)
A=0.19159 (3211/16760, 8.3KJPN)
A=0.1907 (1221/6404, 1000G_30x)
A=0.1879 (941/5008, 1000G)
A=0.1596 (715/4480, Estonian)
A=0.1632 (629/3854, ALSPAC)
A=0.1650 (612/3708, TWINSUK)
A=0.1751 (513/2930, KOREAN)
A=0.1756 (366/2084, HGDP_Stanford)
A=0.2101 (374/1780, HapMap)
A=0.161 (161/998, GoNL)
A=0.142 (85/600, NorthernSweden)
A=0.134 (29/216, Qatari)
G=0.423 (82/194, SGDP_PRJ)
A=0.23 (9/40, GENOME_DK)
G=0.41 (9/22, Siberian)
A=0.0 (0/2, Ancient Sardinia)
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 67802 G=0.83776 A=0.16224
European Sub 55506 G=0.84301 A=0.15699
African Sub 4500 G=0.7640 A=0.2360
African Others Sub 170 G=0.782 A=0.218
African American Sub 4330 G=0.7633 A=0.2367
Asian Sub 186 G=0.871 A=0.129
East Asian Sub 146 G=0.870 A=0.130
Other Asian Sub 40 G=0.88 A=0.12
Latin American 1 Sub 246 G=0.862 A=0.138
Latin American 2 Sub 1226 G=0.7675 A=0.2325
South Asian Sub 4952 G=0.8649 A=0.1351
Other Sub 1186 G=0.8212 A=0.1788


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=0.806090 A=0.193910
gnomAD - Genomes Global Study-wide 140098 G=0.813438 A=0.186562
gnomAD - Genomes European Sub 75910 G=0.84433 A=0.15567
gnomAD - Genomes African Sub 41970 G=0.76107 A=0.23893
gnomAD - Genomes American Sub 13612 G=0.78710 A=0.21290
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.8586 A=0.1414
gnomAD - Genomes East Asian Sub 3130 G=0.8144 A=0.1856
gnomAD - Genomes Other Sub 2152 G=0.8406 A=0.1594
Allele Frequency Aggregator Total Global 67802 G=0.83776 A=0.16224
Allele Frequency Aggregator European Sub 55506 G=0.84301 A=0.15699
Allele Frequency Aggregator South Asian Sub 4952 G=0.8649 A=0.1351
Allele Frequency Aggregator African Sub 4500 G=0.7640 A=0.2360
Allele Frequency Aggregator Latin American 2 Sub 1226 G=0.7675 A=0.2325
Allele Frequency Aggregator Other Sub 1186 G=0.8212 A=0.1788
Allele Frequency Aggregator Latin American 1 Sub 246 G=0.862 A=0.138
Allele Frequency Aggregator Asian Sub 186 G=0.871 A=0.129
14KJPN JAPANESE Study-wide 28258 G=0.81142 A=0.18858
8.3KJPN JAPANESE Study-wide 16760 G=0.80841 A=0.19159
1000Genomes_30x Global Study-wide 6404 G=0.8093 A=0.1907
1000Genomes_30x African Sub 1786 G=0.7419 A=0.2581
1000Genomes_30x Europe Sub 1266 G=0.8697 A=0.1303
1000Genomes_30x South Asian Sub 1202 G=0.8910 A=0.1090
1000Genomes_30x East Asian Sub 1170 G=0.7786 A=0.2214
1000Genomes_30x American Sub 980 G=0.791 A=0.209
1000Genomes Global Study-wide 5008 G=0.8121 A=0.1879
1000Genomes African Sub 1322 G=0.7428 A=0.2572
1000Genomes East Asian Sub 1008 G=0.7827 A=0.2173
1000Genomes Europe Sub 1006 G=0.8708 A=0.1292
1000Genomes South Asian Sub 978 G=0.892 A=0.108
1000Genomes American Sub 694 G=0.790 A=0.210
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8404 A=0.1596
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8368 A=0.1632
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8350 A=0.1650
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.8249 A=0.1751
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.8244 A=0.1756
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.785 A=0.215
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.853 A=0.147
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.846 A=0.154
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.844 A=0.156
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.839 A=0.161
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.759 A=0.241
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.88 A=0.12
HapMap Global Study-wide 1780 G=0.7899 A=0.2101
HapMap American Sub 770 G=0.812 A=0.188
HapMap African Sub 582 G=0.718 A=0.282
HapMap Asian Sub 252 G=0.806 A=0.194
HapMap Europe Sub 176 G=0.909 A=0.091
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.839 A=0.161
Northern Sweden ACPOP Study-wide 600 G=0.858 A=0.142
Qatari Global Study-wide 216 G=0.866 A=0.134
SGDP_PRJ Global Study-wide 194 G=0.423 A=0.577
The Danish reference pan genome Danish Study-wide 40 G=0.78 A=0.23
Siberian Global Study-wide 22 G=0.41 A=0.59
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 2 G=1.0 A=0.0
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 4 NC_000004.12:g.153428862G>A
GRCh37.p13 chr 4 NC_000004.11:g.154350014G>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 G= A
GRCh38.p14 chr 4 NC_000004.12:g.153428862= NC_000004.12:g.153428862G>A
GRCh37.p13 chr 4 NC_000004.11:g.154350014= NC_000004.11:g.154350014G>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#.

85 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss13849030 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss19569793 Feb 27, 2004 (120)
3 ABI ss44497239 Mar 14, 2006 (126)
4 ILLUMINA ss66539173 Nov 30, 2006 (127)
5 ILLUMINA ss66863817 Nov 30, 2006 (127)
6 ILLUMINA ss66932752 Nov 30, 2006 (127)
7 ILLUMINA ss70355902 May 17, 2007 (127)
8 ILLUMINA ss70459168 May 25, 2008 (130)
9 ILLUMINA ss70979722 May 17, 2007 (127)
10 ILLUMINA ss75748546 Dec 06, 2007 (129)
11 KRIBB_YJKIM ss84887977 Dec 15, 2007 (130)
12 BCMHGSC_JDW ss92833889 Mar 24, 2008 (129)
13 ILLUMINA ss121251730 Dec 01, 2009 (131)
14 ENSEMBL ss133300876 Dec 01, 2009 (131)
15 ENSEMBL ss139966858 Dec 01, 2009 (131)
16 ILLUMINA ss152538465 Dec 01, 2009 (131)
17 ILLUMINA ss159103026 Dec 01, 2009 (131)
18 ILLUMINA ss169205439 Jul 04, 2010 (132)
19 ILLUMINA ss169489910 Jul 04, 2010 (132)
20 1000GENOMES ss211516121 Jul 14, 2010 (132)
21 1000GENOMES ss221298162 Jul 14, 2010 (132)
22 1000GENOMES ss232661499 Jul 14, 2010 (132)
23 1000GENOMES ss239895390 Jul 15, 2010 (132)
24 GMI ss277995664 May 04, 2012 (137)
25 GMI ss285035101 Apr 25, 2013 (138)
26 PJP ss293227854 May 09, 2011 (134)
27 ILLUMINA ss536564166 Sep 08, 2015 (146)
28 TISHKOFF ss557955372 Apr 25, 2013 (138)
29 SSMP ss651776288 Apr 25, 2013 (138)
30 ILLUMINA ss825325633 Apr 01, 2015 (144)
31 ILLUMINA ss832615822 Jul 13, 2019 (153)
32 EVA-GONL ss980850556 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1072084604 Aug 21, 2014 (142)
34 1000GENOMES ss1312469461 Aug 21, 2014 (142)
35 DDI ss1430103478 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1580842202 Apr 01, 2015 (144)
37 EVA_DECODE ss1590363853 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1611516696 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1654510729 Apr 01, 2015 (144)
40 EVA_SVP ss1712716929 Apr 01, 2015 (144)
41 HAMMER_LAB ss1802420429 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1924089536 Feb 12, 2016 (147)
43 GENOMED ss1969909856 Jul 19, 2016 (147)
44 JJLAB ss2022630375 Sep 14, 2016 (149)
45 USC_VALOUEV ss2150763470 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2268489379 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2625811078 Nov 08, 2017 (151)
48 GRF ss2706261268 Nov 08, 2017 (151)
49 GNOMAD ss2817145701 Nov 08, 2017 (151)
50 SWEGEN ss2995819554 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3025092084 Nov 08, 2017 (151)
52 CSHL ss3346035839 Nov 08, 2017 (151)
53 ILLUMINA ss3629096946 Oct 12, 2018 (152)
54 ILLUMINA ss3638519574 Oct 12, 2018 (152)
55 ILLUMINA ss3639261806 Oct 12, 2018 (152)
56 ILLUMINA ss3639652992 Oct 12, 2018 (152)
57 ILLUMINA ss3643468409 Oct 12, 2018 (152)
58 URBANLAB ss3647885914 Oct 12, 2018 (152)
59 EGCUT_WGS ss3663728969 Jul 13, 2019 (153)
60 EVA_DECODE ss3713377507 Jul 13, 2019 (153)
61 ACPOP ss3731748483 Jul 13, 2019 (153)
62 EVA ss3762608604 Jul 13, 2019 (153)
63 PACBIO ss3784907335 Jul 13, 2019 (153)
64 PACBIO ss3790336664 Jul 13, 2019 (153)
65 PACBIO ss3795212247 Jul 13, 2019 (153)
66 KHV_HUMAN_GENOMES ss3805767564 Jul 13, 2019 (153)
67 EVA ss3828888817 Apr 26, 2020 (154)
68 HGDP ss3847769304 Apr 26, 2020 (154)
69 SGDP_PRJ ss3860398259 Apr 26, 2020 (154)
70 KRGDB ss3906749157 Apr 26, 2020 (154)
71 EVA ss3985103788 Apr 26, 2021 (155)
72 EVA ss4017175717 Apr 26, 2021 (155)
73 TOPMED ss4637757572 Apr 26, 2021 (155)
74 TOMMO_GENOMICS ss5168748479 Apr 26, 2021 (155)
75 1000G_HIGH_COVERAGE ss5261593589 Oct 17, 2022 (156)
76 EVA ss5353344558 Oct 17, 2022 (156)
77 HUGCELL_USP ss5460086906 Oct 17, 2022 (156)
78 1000G_HIGH_COVERAGE ss5543994496 Oct 17, 2022 (156)
79 SANFORD_IMAGENETICS ss5636426703 Oct 17, 2022 (156)
80 TOMMO_GENOMICS ss5703946763 Oct 17, 2022 (156)
81 YY_MCH ss5805678088 Oct 17, 2022 (156)
82 EVA ss5844937872 Oct 17, 2022 (156)
83 EVA ss5854511214 Oct 17, 2022 (156)
84 EVA ss5866156593 Oct 17, 2022 (156)
85 EVA ss5964832942 Oct 17, 2022 (156)
86 1000Genomes NC_000004.11 - 154350014 Oct 12, 2018 (152)
87 1000Genomes_30x NC_000004.12 - 153428862 Oct 17, 2022 (156)
88 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 154350014 Oct 12, 2018 (152)
89 Genetic variation in the Estonian population NC_000004.11 - 154350014 Oct 12, 2018 (152)
90 The Danish reference pan genome NC_000004.11 - 154350014 Apr 26, 2020 (154)
91 gnomAD - Genomes NC_000004.12 - 153428862 Apr 26, 2021 (155)
92 Genome of the Netherlands Release 5 NC_000004.11 - 154350014 Apr 26, 2020 (154)
93 HGDP-CEPH-db Supplement 1 NC_000004.10 - 154569464 Apr 26, 2020 (154)
94 HapMap NC_000004.12 - 153428862 Apr 26, 2020 (154)
95 KOREAN population from KRGDB NC_000004.11 - 154350014 Apr 26, 2020 (154)
96 Northern Sweden NC_000004.11 - 154350014 Jul 13, 2019 (153)
97 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000004.11 - 154350014 Apr 26, 2021 (155)
98 Qatari NC_000004.11 - 154350014 Apr 26, 2020 (154)
99 SGDP_PRJ NC_000004.11 - 154350014 Apr 26, 2020 (154)
100 Siberian NC_000004.11 - 154350014 Apr 26, 2020 (154)
101 8.3KJPN NC_000004.11 - 154350014 Apr 26, 2021 (155)
102 14KJPN NC_000004.12 - 153428862 Oct 17, 2022 (156)
103 TopMed NC_000004.12 - 153428862 Apr 26, 2021 (155)
104 UK 10K study - Twins NC_000004.11 - 154350014 Oct 12, 2018 (152)
105 ALFA NC_000004.12 - 153428862 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)
rs59927420 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3639261806, ss3639652992 NC_000004.9:154707618:G:A NC_000004.12:153428861:G:A (self)
447196, ss92833889, ss211516121, ss277995664, ss285035101, ss293227854, ss825325633, ss1590363853, ss1712716929, ss3643468409, ss3847769304 NC_000004.10:154569463:G:A NC_000004.12:153428861:G:A (self)
23969141, 13330283, 9467217, 7007141, 5904091, 13926551, 5033348, 329715, 6131466, 12415239, 3279824, 26717786, 13330283, ss221298162, ss232661499, ss239895390, ss536564166, ss557955372, ss651776288, ss832615822, ss980850556, ss1072084604, ss1312469461, ss1430103478, ss1580842202, ss1611516696, ss1654510729, ss1802420429, ss1924089536, ss1969909856, ss2022630375, ss2150763470, ss2625811078, ss2706261268, ss2817145701, ss2995819554, ss3346035839, ss3629096946, ss3638519574, ss3663728969, ss3731748483, ss3762608604, ss3784907335, ss3790336664, ss3795212247, ss3828888817, ss3860398259, ss3906749157, ss3985103788, ss4017175717, ss5168748479, ss5353344558, ss5636426703, ss5844937872, ss5964832942 NC_000004.11:154350013:G:A NC_000004.12:153428861:G:A (self)
31520431, 169795808, 2737517, 37783867, 475135128, 11294254567, ss2268489379, ss3025092084, ss3647885914, ss3713377507, ss3805767564, ss4637757572, ss5261593589, ss5460086906, ss5543994496, ss5703946763, ss5805678088, ss5854511214, ss5866156593 NC_000004.12:153428861:G:A NC_000004.12:153428861:G:A (self)
ss44497239, ss66539173, ss66863817, ss66932752, ss70355902, ss70459168, ss70979722, ss75748546, ss84887977, ss121251730, ss133300876, ss139966858, ss152538465, ss159103026, ss169205439, ss169489910 NT_016354.19:78897734:G:A NC_000004.12:153428861:G:A (self)
ss13849030, ss19569793 NT_016606.16:15898069:G:A NC_000004.12:153428861: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 rs10003241

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