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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.

rs3828570

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:601532 (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 / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.401417 (106251/264690, TOPMED)
G=0.385511 (53977/140014, GnomAD)
A=0.42455 (11997/28258, 14KJPN) (+ 17 more)
A=0.42834 (7179/16760, 8.3KJPN)
G=0.45969 (5520/12008, ALFA)
G=0.4653 (2980/6404, 1000G_30x)
G=0.4740 (2374/5008, 1000G)
G=0.3533 (1583/4480, Estonian)
G=0.3599 (1387/3854, ALSPAC)
G=0.3546 (1315/3708, TWINSUK)
A=0.3782 (1108/2930, KOREAN)
G=0.4915 (930/1892, HapMap)
G=0.377 (376/998, GoNL)
G=0.307 (184/600, NorthernSweden)
G=0.283 (127/448, SGDP_PRJ)
A=0.472 (102/216, Qatari)
A=0.231 (49/212, Vietnamese)
G=0.37 (34/92, Ancient Sardinia)
G=0.32 (14/44, Siberian)
G=0.40 (16/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105374608 : Intron Variant
Publications
1 citation
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 12008 G=0.45969 A=0.54031, C=0.00000, T=0.00000
European Sub 9248 G=0.4233 A=0.5767, C=0.0000, T=0.0000
African Sub 1802 G=0.5649 A=0.4351, C=0.0000, T=0.0000
African Others Sub 52 G=0.56 A=0.44, C=0.00, T=0.00
African American Sub 1750 G=0.5651 A=0.4349, C=0.0000, T=0.0000
Asian Sub 84 G=0.93 A=0.07, C=0.00, T=0.00
East Asian Sub 60 G=0.90 A=0.10, C=0.00, T=0.00
Other Asian Sub 24 G=1.00 A=0.00, C=0.00, T=0.00
Latin American 1 Sub 46 G=0.80 A=0.20, C=0.00, T=0.00
Latin American 2 Sub 170 G=0.829 A=0.171, C=0.000, T=0.000
South Asian Sub 28 G=1.00 A=0.00, C=0.00, T=0.00
Other Sub 630 G=0.481 A=0.519, C=0.000, T=0.000


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=0.401417 A=0.598583
gnomAD - Genomes Global Study-wide 140014 G=0.385511 A=0.614489
gnomAD - Genomes European Sub 75854 G=0.35626 A=0.64374
gnomAD - Genomes African Sub 41920 G=0.41176 A=0.58824
gnomAD - Genomes American Sub 13638 G=0.39815 A=0.60185
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.4157 A=0.5843
gnomAD - Genomes East Asian Sub 3128 G=0.6435 A=0.3565
gnomAD - Genomes Other Sub 2152 G=0.4033 A=0.5967
14KJPN JAPANESE Study-wide 28258 G=0.57545 A=0.42455
8.3KJPN JAPANESE Study-wide 16760 G=0.57166 A=0.42834
Allele Frequency Aggregator Total Global 12008 G=0.45969 A=0.54031, C=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 9248 G=0.4233 A=0.5767, C=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 1802 G=0.5649 A=0.4351, C=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 630 G=0.481 A=0.519, C=0.000, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 170 G=0.829 A=0.171, C=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 84 G=0.93 A=0.07, C=0.00, T=0.00
Allele Frequency Aggregator Latin American 1 Sub 46 G=0.80 A=0.20, C=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 28 G=1.00 A=0.00, C=0.00, T=0.00
1000Genomes_30x Global Study-wide 6404 G=0.4653 A=0.5347
1000Genomes_30x African Sub 1786 G=0.4362 A=0.5638
1000Genomes_30x Europe Sub 1266 G=0.3602 A=0.6398
1000Genomes_30x South Asian Sub 1202 G=0.4285 A=0.5715
1000Genomes_30x East Asian Sub 1170 G=0.6675 A=0.3325
1000Genomes_30x American Sub 980 G=0.458 A=0.542
1000Genomes Global Study-wide 5008 G=0.4740 A=0.5260
1000Genomes African Sub 1322 G=0.4470 A=0.5530
1000Genomes East Asian Sub 1008 G=0.6716 A=0.3284
1000Genomes Europe Sub 1006 G=0.3598 A=0.6402
1000Genomes South Asian Sub 978 G=0.434 A=0.566
1000Genomes American Sub 694 G=0.461 A=0.539
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.3533 A=0.6467
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.3599 A=0.6401
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.3546 A=0.6454
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6218 A=0.3782
HapMap Global Study-wide 1892 G=0.4915 A=0.5085
HapMap American Sub 770 G=0.486 A=0.514
HapMap African Sub 692 G=0.481 A=0.519
HapMap Asian Sub 254 G=0.650 A=0.350
HapMap Europe Sub 176 G=0.330 A=0.670
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.377 A=0.623
Northern Sweden ACPOP Study-wide 600 G=0.307 A=0.693
SGDP_PRJ Global Study-wide 448 G=0.283 A=0.717
Qatari Global Study-wide 216 G=0.528 A=0.472
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.769 A=0.231
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 92 G=0.37 A=0.63
Siberian Global Study-wide 44 G=0.32 A=0.68
The Danish reference pan genome Danish Study-wide 40 G=0.40 A=0.60
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.601532G>A
GRCh38.p14 chr 5 NC_000005.10:g.601532G>C
GRCh38.p14 chr 5 NC_000005.10:g.601532G>T
GRCh37.p13 chr 5 NC_000005.9:g.601647G>A
GRCh37.p13 chr 5 NC_000005.9:g.601647G>C
GRCh37.p13 chr 5 NC_000005.9:g.601647G>T
GRCh38.p14 chr 5 alt locus HSCHR5_5_CTG1 NT_187550.1:g.25365C>T
GRCh38.p14 chr 5 alt locus HSCHR5_5_CTG1 NT_187550.1:g.25365C>G
GRCh38.p14 chr 5 alt locus HSCHR5_5_CTG1 NT_187550.1:g.25365C>A
Gene: LOC105374608, uncharacterized LOC105374608 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105374608 transcript variant X1 XR_007058672.1:n. N/A Intron Variant
LOC105374608 transcript variant X2 XR_007058673.1:n. N/A Intron Variant
LOC105374608 transcript variant X3 XR_007058674.1:n. N/A Intron Variant
LOC105374608 transcript variant X4 XR_007058675.1:n. N/A Intron Variant
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 C T
GRCh38.p14 chr 5 NC_000005.10:g.601532= NC_000005.10:g.601532G>A NC_000005.10:g.601532G>C NC_000005.10:g.601532G>T
GRCh37.p13 chr 5 NC_000005.9:g.601647= NC_000005.9:g.601647G>A NC_000005.9:g.601647G>C NC_000005.9:g.601647G>T
GRCh38.p14 chr 5 alt locus HSCHR5_5_CTG1 NT_187550.1:g.25365= NT_187550.1:g.25365C>T NT_187550.1:g.25365C>G NT_187550.1:g.25365C>A
FLJ20413 transcript NM_017808.1:c.*212= NM_017808.1:c.*212C>T NM_017808.1:c.*212C>G NM_017808.1:c.*212C>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#.

88 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss5015066 Aug 28, 2002 (107)
2 WI_SSAHASNP ss6859477 Feb 20, 2003 (111)
3 WI_SSAHASNP ss14644296 Dec 05, 2003 (119)
4 PERLEGEN ss24667095 Sep 20, 2004 (123)
5 ILLUMINA ss75138407 Dec 06, 2007 (129)
6 HGSV ss84721181 Dec 14, 2007 (130)
7 BCMHGSC_JDW ss92956485 Mar 24, 2008 (129)
8 1000GENOMES ss108728991 Jan 23, 2009 (130)
9 1000GENOMES ss111284339 Jan 25, 2009 (130)
10 ILLUMINA-UK ss116425343 Feb 14, 2009 (130)
11 KRIBB_YJKIM ss119466507 Dec 01, 2009 (131)
12 ILLUMINA ss120243052 Dec 01, 2009 (131)
13 ENSEMBL ss142760891 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss161942726 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss164012616 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss165987999 Jul 04, 2010 (132)
17 ILLUMINA ss173657887 Jul 04, 2010 (132)
18 BUSHMAN ss199758672 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss206858001 Jul 04, 2010 (132)
20 1000GENOMES ss221463379 Jul 14, 2010 (132)
21 1000GENOMES ss232789743 Jul 14, 2010 (132)
22 1000GENOMES ss239995019 Jul 15, 2010 (132)
23 ILLUMINA ss244256897 Jul 04, 2010 (132)
24 BL ss253142363 May 09, 2011 (134)
25 GMI ss278130696 May 04, 2012 (137)
26 GMI ss285102087 Apr 25, 2013 (138)
27 PJP ss293339234 May 09, 2011 (134)
28 ILLUMINA ss410931029 Sep 17, 2011 (135)
29 ILLUMINA ss537201767 Sep 08, 2015 (146)
30 TISHKOFF ss558142346 Apr 25, 2013 (138)
31 SSMP ss651984414 Apr 25, 2013 (138)
32 EVA-GONL ss981157090 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1072321951 Aug 21, 2014 (142)
34 1000GENOMES ss1313574798 Aug 21, 2014 (142)
35 DDI ss1430213942 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1580973792 Apr 01, 2015 (144)
37 EVA_DECODE ss1590674274 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1612098637 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1655092670 Apr 01, 2015 (144)
40 EVA_SVP ss1712736606 Apr 01, 2015 (144)
41 HAMMER_LAB ss1802906459 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1924411515 Feb 12, 2016 (147)
43 GENOMED ss1969990055 Jul 19, 2016 (147)
44 JJLAB ss2022800086 Sep 14, 2016 (149)
45 ILLUMINA ss2094937367 Dec 20, 2016 (150)
46 ILLUMINA ss2095152535 Dec 20, 2016 (150)
47 USC_VALOUEV ss2150949086 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2270718676 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2625898424 Nov 08, 2017 (151)
50 GRF ss2706468749 Nov 08, 2017 (151)
51 GNOMAD ss2820239189 Nov 08, 2017 (151)
52 SWEGEN ss2996301093 Nov 08, 2017 (151)
53 BIOINF_KMB_FNS_UNIBA ss3025183033 Nov 08, 2017 (151)
54 CSHL ss3346195766 Nov 08, 2017 (151)
55 ILLUMINA ss3629157978 Oct 12, 2018 (152)
56 ILLUMINA ss3638533486 Oct 12, 2018 (152)
57 ILLUMINA ss3643481031 Oct 12, 2018 (152)
58 ILLUMINA ss3652949579 Oct 12, 2018 (152)
59 EGCUT_WGS ss3664195307 Jul 13, 2019 (153)
60 EVA_DECODE ss3713939318 Jul 13, 2019 (153)
61 ACPOP ss3732010514 Jul 13, 2019 (153)
62 EVA ss3762957570 Jul 13, 2019 (153)
63 PACBIO ss3784997150 Jul 13, 2019 (153)
64 PACBIO ss3790417361 Jul 13, 2019 (153)
65 PACBIO ss3795293796 Jul 13, 2019 (153)
66 KHV_HUMAN_GENOMES ss3806127164 Jul 13, 2019 (153)
67 EVA ss3829048922 Apr 26, 2020 (154)
68 EVA ss3837983604 Apr 26, 2020 (154)
69 EVA ss3843426066 Apr 26, 2020 (154)
70 SGDP_PRJ ss3861020517 Apr 26, 2020 (154)
71 KRGDB ss3907454469 Apr 26, 2020 (154)
72 EVA ss3985119340 Apr 26, 2021 (155)
73 EVA ss4017188420 Apr 26, 2021 (155)
74 VINODS ss4024244341 Apr 26, 2021 (155)
75 TOPMED ss4646958167 Apr 26, 2021 (155)
76 TOMMO_GENOMICS ss5170005390 Apr 26, 2021 (155)
77 1000G_HIGH_COVERAGE ss5262580926 Oct 13, 2022 (156)
78 EVA ss5355113671 Oct 13, 2022 (156)
79 HUGCELL_USP ss5460963151 Oct 13, 2022 (156)
80 EVA ss5507889323 Oct 13, 2022 (156)
81 1000G_HIGH_COVERAGE ss5545490543 Oct 13, 2022 (156)
82 SANFORD_IMAGENETICS ss5637009657 Oct 13, 2022 (156)
83 TOMMO_GENOMICS ss5705570305 Oct 13, 2022 (156)
84 YY_MCH ss5805943819 Oct 13, 2022 (156)
85 EVA ss5834397344 Oct 13, 2022 (156)
86 EVA ss5854642632 Oct 13, 2022 (156)
87 EVA ss5892658106 Oct 13, 2022 (156)
88 EVA ss5965420554 Oct 13, 2022 (156)
89 1000Genomes NC_000005.9 - 601647 Oct 12, 2018 (152)
90 1000Genomes_30x NC_000005.10 - 601532 Oct 13, 2022 (156)
91 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 601647 Oct 12, 2018 (152)
92 Genetic variation in the Estonian population NC_000005.9 - 601647 Oct 12, 2018 (152)
93 The Danish reference pan genome NC_000005.9 - 601647 Apr 26, 2020 (154)
94 gnomAD - Genomes NC_000005.10 - 601532 Apr 26, 2021 (155)
95 Genome of the Netherlands Release 5 NC_000005.9 - 601647 Apr 26, 2020 (154)
96 HapMap NC_000005.10 - 601532 Apr 26, 2020 (154)
97 KOREAN population from KRGDB NC_000005.9 - 601647 Apr 26, 2020 (154)
98 Northern Sweden NC_000005.9 - 601647 Jul 13, 2019 (153)
99 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000005.9 - 601647 Apr 26, 2021 (155)
100 Qatari NC_000005.9 - 601647 Apr 26, 2020 (154)
101 SGDP_PRJ NC_000005.9 - 601647 Apr 26, 2020 (154)
102 Siberian NC_000005.9 - 601647 Apr 26, 2020 (154)
103 8.3KJPN NC_000005.9 - 601647 Apr 26, 2021 (155)
104 14KJPN NC_000005.10 - 601532 Oct 13, 2022 (156)
105 TopMed NC_000005.10 - 601532 Apr 26, 2021 (155)
106 UK 10K study - Twins NC_000005.9 - 601647 Oct 12, 2018 (152)
107 A Vietnamese Genetic Variation Database NC_000005.9 - 601647 Jul 13, 2019 (153)
108 ALFA NC_000005.10 - 601532 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)
rs17524505 Oct 08, 2004 (123)
rs57146775 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84721181, ss92956485, ss108728991, ss111284339, ss116425343, ss161942726, ss164012616, ss165987999, ss199758672, ss206858001, ss253142363, ss278130696, ss285102087, ss293339234, ss1590674274, ss1712736606, ss2094937367, ss3643481031 NC_000005.8:654646:G:A NC_000005.10:601531:G:A (self)
25118083, 13972795, 9933555, 7138731, 6201550, 14631863, 5295379, 345267, 6453445, 13037497, 3465440, 27974697, 13972795, 3097910, ss221463379, ss232789743, ss239995019, ss537201767, ss558142346, ss651984414, ss981157090, ss1072321951, ss1313574798, ss1430213942, ss1580973792, ss1612098637, ss1655092670, ss1802906459, ss1924411515, ss1969990055, ss2022800086, ss2095152535, ss2150949086, ss2625898424, ss2706468749, ss2820239189, ss2996301093, ss3346195766, ss3629157978, ss3638533486, ss3652949579, ss3664195307, ss3732010514, ss3762957570, ss3784997150, ss3790417361, ss3795293796, ss3829048922, ss3837983604, ss3861020517, ss3907454469, ss3985119340, ss4017188420, ss5170005390, ss5355113671, ss5507889323, ss5637009657, ss5834397344, ss5965420554 NC_000005.9:601646:G:A NC_000005.10:601531:G:A (self)
33016478, 177645573, 2789306, 39407409, 484335724, 4215132872, ss2270718676, ss3025183033, ss3713939318, ss3806127164, ss3843426066, ss4646958167, ss5262580926, ss5460963151, ss5545490543, ss5705570305, ss5805943819, ss5854642632, ss5892658106 NC_000005.10:601531:G:A NC_000005.10:601531:G:A (self)
ss5015066, ss6859477, ss24667095, ss75138407, ss119466507, ss120243052, ss142760891, ss173657887, ss244256897, ss410931029 NT_006576.16:591646:G:A NC_000005.10:601531:G:A (self)
ss14644296 NT_023089.13:584384:G:A NC_000005.10:601531:G:A (self)
ss4024244341 NT_187550.1:25364:C:T NC_000005.10:601531:G:A (self)
4215132872 NC_000005.10:601531:G:C NC_000005.10:601531:G:C (self)
4215132872 NC_000005.10:601531:G:T NC_000005.10:601531:G:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs3828570
PMID Title Author Year Journal
19324860 An international collaborative family-based whole-genome linkage scan for high-grade myopia. Li YJ et al. 2009 Investigative ophthalmology & visual science
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