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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.

rs7556670

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:109273925 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.298156 (78919/264690, TOPMED)
A=0.37574 (10617/28256, 14KJPN)
A=0.23140 (4161/17982, ALFA) (+ 16 more)
A=0.37506 (6286/16760, 8.3KJPN)
A=0.2993 (1917/6404, 1000G_30x)
A=0.3069 (1537/5008, 1000G)
A=0.3502 (1569/4480, Estonian)
A=0.3765 (1451/3854, ALSPAC)
A=0.3843 (1425/3708, TWINSUK)
A=0.3904 (1144/2930, KOREAN)
A=0.2654 (501/1888, HapMap)
A=0.4023 (737/1832, Korea1K)
A=0.363 (362/998, GoNL)
A=0.397 (238/600, NorthernSweden)
G=0.427 (128/300, SGDP_PRJ)
A=0.287 (62/216, Qatari)
A=0.41 (34/82, Ancient Sardinia)
G=0.42 (17/40, GENOME_DK)
G=0.39 (14/36, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SH3RF3 : Intron Variant
RANBP2 : Intron Variant
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 17982 G=0.76860 A=0.23140, T=0.00000
European Sub 11060 G=0.73418 A=0.26582, T=0.00000
African Sub 3022 G=0.9672 A=0.0328, T=0.0000
African Others Sub 114 G=0.982 A=0.018, T=0.000
African American Sub 2908 G=0.9666 A=0.0334, T=0.0000
Asian Sub 108 G=0.917 A=0.083, T=0.000
East Asian Sub 62 G=0.90 A=0.10, T=0.00
Other Asian Sub 46 G=0.93 A=0.07, T=0.00
Latin American 1 Sub 216 G=0.838 A=0.162, T=0.000
Latin American 2 Sub 2388 G=0.6717 A=0.3283, T=0.0000
South Asian Sub 44 G=0.86 A=0.14, T=0.00
Other Sub 1144 G=0.7483 A=0.2517, T=0.0000


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=0.701844 A=0.298156
14KJPN JAPANESE Study-wide 28256 G=0.62426 A=0.37574
Allele Frequency Aggregator Total Global 17982 G=0.76860 A=0.23140, T=0.00000
Allele Frequency Aggregator European Sub 11060 G=0.73418 A=0.26582, T=0.00000
Allele Frequency Aggregator African Sub 3022 G=0.9672 A=0.0328, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 2388 G=0.6717 A=0.3283, T=0.0000
Allele Frequency Aggregator Other Sub 1144 G=0.7483 A=0.2517, T=0.0000
Allele Frequency Aggregator Latin American 1 Sub 216 G=0.838 A=0.162, T=0.000
Allele Frequency Aggregator Asian Sub 108 G=0.917 A=0.083, T=0.000
Allele Frequency Aggregator South Asian Sub 44 G=0.86 A=0.14, T=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.62494 A=0.37506
1000Genomes_30x Global Study-wide 6404 G=0.7007 A=0.2993
1000Genomes_30x African Sub 1786 G=0.9373 A=0.0627
1000Genomes_30x Europe Sub 1266 G=0.6114 A=0.3886
1000Genomes_30x South Asian Sub 1202 G=0.5582 A=0.4418
1000Genomes_30x East Asian Sub 1170 G=0.6145 A=0.3855
1000Genomes_30x American Sub 980 G=0.662 A=0.338
1000Genomes Global Study-wide 5008 G=0.6931 A=0.3069
1000Genomes African Sub 1322 G=0.9372 A=0.0628
1000Genomes East Asian Sub 1008 G=0.6181 A=0.3819
1000Genomes Europe Sub 1006 G=0.6103 A=0.3897
1000Genomes South Asian Sub 978 G=0.545 A=0.455
1000Genomes American Sub 694 G=0.666 A=0.334
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6498 A=0.3502
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6235 A=0.3765
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6157 A=0.3843
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6096 A=0.3904
HapMap Global Study-wide 1888 G=0.7346 A=0.2654
HapMap American Sub 768 G=0.668 A=0.332
HapMap African Sub 690 G=0.886 A=0.114
HapMap Asian Sub 254 G=0.610 A=0.390
HapMap Europe Sub 176 G=0.614 A=0.386
Korean Genome Project KOREAN Study-wide 1832 G=0.5977 A=0.4023
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.637 A=0.363
Northern Sweden ACPOP Study-wide 600 G=0.603 A=0.397
SGDP_PRJ Global Study-wide 300 G=0.427 A=0.573
Qatari Global Study-wide 216 G=0.713 A=0.287
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 82 G=0.59 A=0.41
The Danish reference pan genome Danish Study-wide 40 G=0.42 A=0.57
Siberian Global Study-wide 36 G=0.39 A=0.61
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 2 NC_000002.12:g.109273925G>A
GRCh38.p14 chr 2 NC_000002.12:g.109273925G>T
GRCh37.p13 chr 2 NC_000002.11:g.109890381G>A
GRCh37.p13 chr 2 NC_000002.11:g.109890381G>T
Gene: SH3RF3, SH3 domain containing ring finger 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SH3RF3 transcript NM_001099289.3:c.574-7374…

NM_001099289.3:c.574-73749G>A

 		N/A Intron Variant
SH3RF3 transcript variant X1 XM_011511109.3:c.574-7374…

XM_011511109.3:c.574-73749G>A

 		N/A Intron Variant
SH3RF3 transcript variant X3 XM_011511110.3:c. N/A Genic Upstream Transcript Variant
SH3RF3 transcript variant X2 XM_047444144.1:c. N/A Genic Upstream Transcript Variant
Gene: RANBP2, RAN binding protein 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RANBP2 transcript variant 1 NM_006267.5:c. N/A Genic Downstream Transcript Variant
RANBP2 transcript variant X4 XM_047445367.1:c.8370+500…

XM_047445367.1:c.8370+500879G>A

 		N/A Intron Variant
RANBP2 transcript variant X1 XM_005264002.4:c. N/A Genic Downstream Transcript Variant
RANBP2 transcript variant X3 XM_005264003.4:c. N/A Genic Downstream Transcript Variant
RANBP2 transcript variant X4 XM_005264004.4:c. N/A Genic Downstream Transcript Variant
RANBP2 transcript variant X5 XM_005264007.4:c. N/A Genic Downstream Transcript Variant
RANBP2 transcript variant X2 XM_011511575.3:c. N/A Genic Downstream Transcript Variant
RANBP2 transcript variant X3 XM_011511576.4:c. N/A Genic Downstream Transcript Variant
RANBP2 transcript variant X6 XM_011511578.3:c. N/A Genic Downstream Transcript Variant
RANBP2 transcript variant X7 XM_017004624.3:c. N/A Genic Downstream Transcript Variant
RANBP2 transcript variant X8 XM_017004625.2:c. N/A Genic Downstream Transcript Variant
RANBP2 transcript variant X5 XM_047445366.1:c. N/A Genic Downstream Transcript 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 T
GRCh38.p14 chr 2 NC_000002.12:g.109273925= NC_000002.12:g.109273925G>A NC_000002.12:g.109273925G>T
GRCh37.p13 chr 2 NC_000002.11:g.109890381= NC_000002.11:g.109890381G>A NC_000002.11:g.109890381G>T
SH3RF3 transcript NM_001099289.1:c.574-73749= NM_001099289.1:c.574-73749G>A NM_001099289.1:c.574-73749G>T
SH3RF3 transcript NM_001099289.3:c.574-73749= NM_001099289.3:c.574-73749G>A NM_001099289.3:c.574-73749G>T
SH3RF3 transcript variant X1 XM_011511109.3:c.574-73749= XM_011511109.3:c.574-73749G>A XM_011511109.3:c.574-73749G>T
RANBP2 transcript variant X4 XM_047445367.1:c.8370+500879= XM_047445367.1:c.8370+500879G>A XM_047445367.1:c.8370+500879G>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#.

71 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss11432302 Jul 11, 2003 (116)
2 CSHL-HAPMAP ss16810090 Feb 27, 2004 (120)
3 SSAHASNP ss21557899 Apr 05, 2004 (123)
4 ABI ss44219852 Mar 15, 2006 (126)
5 AFFY ss76608005 Dec 08, 2007 (130)
6 BCMHGSC_JDW ss91291978 Mar 24, 2008 (129)
7 HUMANGENOME_JCVI ss96417207 Feb 05, 2009 (130)
8 KRIBB_YJKIM ss104957036 Feb 05, 2009 (130)
9 1000GENOMES ss109774089 Jan 24, 2009 (130)
10 ENSEMBL ss132805380 Dec 01, 2009 (131)
11 ENSEMBL ss138504967 Dec 01, 2009 (131)
12 GMI ss157489689 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss164970801 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss167008497 Jul 04, 2010 (132)
15 1000GENOMES ss219430663 Jul 14, 2010 (132)
16 1000GENOMES ss231304762 Jul 14, 2010 (132)
17 1000GENOMES ss238827220 Jul 15, 2010 (132)
18 BL ss253362586 May 09, 2011 (134)
19 GMI ss276616697 May 04, 2012 (137)
20 GMI ss284409433 Apr 25, 2013 (138)
21 PJP ss292339721 May 09, 2011 (134)
22 TISHKOFF ss555785003 Apr 25, 2013 (138)
23 SSMP ss649402506 Apr 25, 2013 (138)
24 EVA-GONL ss977206761 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1069384051 Aug 21, 2014 (142)
26 1000GENOMES ss1298721356 Aug 21, 2014 (142)
27 DDI ss1428687904 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1579024358 Apr 01, 2015 (144)
29 EVA_DECODE ss1586631195 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1604262683 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1647256716 Apr 01, 2015 (144)
32 EVA_SVP ss1712480247 Apr 01, 2015 (144)
33 HAMMER_LAB ss1797270808 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1920450713 Feb 12, 2016 (147)
35 GENOMED ss1968852589 Jul 19, 2016 (147)
36 JJLAB ss2020755250 Sep 14, 2016 (149)
37 USC_VALOUEV ss2148811385 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2233169698 Dec 20, 2016 (150)
39 SYSTEMSBIOZJU ss2624883544 Nov 08, 2017 (151)
40 GRF ss2703417943 Nov 08, 2017 (151)
41 GNOMAD ss2777887546 Nov 08, 2017 (151)
42 SWEGEN ss2990161299 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3024139899 Nov 08, 2017 (151)
44 CSHL ss3344402603 Nov 08, 2017 (151)
45 URBANLAB ss3647108885 Oct 11, 2018 (152)
46 EGCUT_WGS ss3658050285 Jul 13, 2019 (153)
47 EVA_DECODE ss3704607370 Jul 13, 2019 (153)
48 ACPOP ss3728738875 Jul 13, 2019 (153)
49 EVA ss3757200622 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3801566295 Jul 13, 2019 (153)
51 EVA ss3827148849 Apr 25, 2020 (154)
52 EVA ss3836986527 Apr 25, 2020 (154)
53 EVA ss3842405232 Apr 25, 2020 (154)
54 SGDP_PRJ ss3853071923 Apr 25, 2020 (154)
55 KRGDB ss3898616923 Apr 25, 2020 (154)
56 KOGIC ss3948655222 Apr 25, 2020 (154)
57 EVA ss3984913615 Apr 26, 2021 (155)
58 TOPMED ss4518763525 Apr 26, 2021 (155)
59 TOMMO_GENOMICS ss5153150702 Apr 26, 2021 (155)
60 1000G_HIGH_COVERAGE ss5249465797 Oct 12, 2022 (156)
61 EVA ss5331340406 Oct 12, 2022 (156)
62 HUGCELL_USP ss5449381267 Oct 12, 2022 (156)
63 EVA ss5506532468 Oct 12, 2022 (156)
64 1000G_HIGH_COVERAGE ss5525451128 Oct 12, 2022 (156)
65 SANFORD_IMAGENETICS ss5629488867 Oct 12, 2022 (156)
66 TOMMO_GENOMICS ss5683064077 Oct 12, 2022 (156)
67 YY_MCH ss5802588565 Oct 12, 2022 (156)
68 EVA ss5820594476 Oct 12, 2022 (156)
69 EVA ss5852658561 Oct 12, 2022 (156)
70 EVA ss5931796137 Oct 12, 2022 (156)
71 EVA ss5955707034 Oct 12, 2022 (156)
72 1000Genomes NC_000002.11 - 109890381 Oct 11, 2018 (152)
73 1000Genomes_30x NC_000002.12 - 109273925 Oct 12, 2022 (156)
74 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 109890381 Oct 11, 2018 (152)
75 Genetic variation in the Estonian population NC_000002.11 - 109890381 Oct 11, 2018 (152)
76 The Danish reference pan genome NC_000002.11 - 109890381 Apr 25, 2020 (154)
77 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 69371219 (NC_000002.12:109273924:G:A 41102/140012)
Row 69371220 (NC_000002.12:109273924:G:T 5/140066)

- Apr 26, 2021 (155)
78 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 69371219 (NC_000002.12:109273924:G:A 41102/140012)
Row 69371220 (NC_000002.12:109273924:G:T 5/140066)

- Apr 26, 2021 (155)
79 Genome of the Netherlands Release 5 NC_000002.11 - 109890381 Apr 25, 2020 (154)
80 HapMap NC_000002.12 - 109273925 Apr 25, 2020 (154)
81 KOREAN population from KRGDB NC_000002.11 - 109890381 Apr 25, 2020 (154)
82 Korean Genome Project NC_000002.12 - 109273925 Apr 25, 2020 (154)
83 Northern Sweden NC_000002.11 - 109890381 Jul 13, 2019 (153)
84 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000002.11 - 109890381 Apr 26, 2021 (155)
85 Qatari NC_000002.11 - 109890381 Apr 25, 2020 (154)
86 SGDP_PRJ NC_000002.11 - 109890381 Apr 25, 2020 (154)
87 Siberian NC_000002.11 - 109890381 Apr 25, 2020 (154)
88 8.3KJPN NC_000002.11 - 109890381 Apr 26, 2021 (155)
89 14KJPN NC_000002.12 - 109273925 Oct 12, 2022 (156)
90 TopMed NC_000002.12 - 109273925 Apr 26, 2021 (155)
91 UK 10K study - Twins NC_000002.11 - 109890381 Oct 11, 2018 (152)
92 ALFA NC_000002.12 - 109273925 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)
rs12986421 Sep 24, 2004 (123)
rs56453654 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss91291978, ss109774089, ss164970801, ss167008497, ss253362586, ss276616697, ss284409433, ss292339721, ss1586631195, ss1712480247 NC_000002.10:109256812:G:A NC_000002.12:109273924:G:A (self)
9716500, 5365000, 3788533, 5191213, 2359008, 5794317, 2023740, 139542, 2492643, 5088903, 1327739, 11120009, 5365000, ss219430663, ss231304762, ss238827220, ss555785003, ss649402506, ss977206761, ss1069384051, ss1298721356, ss1428687904, ss1579024358, ss1604262683, ss1647256716, ss1797270808, ss1920450713, ss1968852589, ss2020755250, ss2148811385, ss2624883544, ss2703417943, ss2777887546, ss2990161299, ss3344402603, ss3658050285, ss3728738875, ss3757200622, ss3827148849, ss3836986527, ss3853071923, ss3898616923, ss3984913615, ss5153150702, ss5331340406, ss5506532468, ss5629488867, ss5820594476, ss5955707034 NC_000002.11:109890380:G:A NC_000002.12:109273924:G:A (self)
12977063, 1865962, 5033223, 16901181, 322586404, 15248094511, ss2233169698, ss3024139899, ss3647108885, ss3704607370, ss3801566295, ss3842405232, ss3948655222, ss4518763525, ss5249465797, ss5449381267, ss5525451128, ss5683064077, ss5802588565, ss5852658561, ss5931796137 NC_000002.12:109273924:G:A NC_000002.12:109273924:G:A (self)
ss11432302, ss16810090, ss21557899 NT_022171.13:11956404:G:A NC_000002.12:109273924:G:A (self)
ss44219852, ss76608005, ss96417207, ss104957036, ss132805380, ss138504967, ss157489689 NT_022171.15:14564209:G:A NC_000002.12:109273924:G:A (self)
15248094511, ss2233169698 NC_000002.12:109273924:G:T NC_000002.12:109273924: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.

No publications for rs7556670

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