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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.

rs3817301

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:120576224 (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=0.077608 (20542/264690, TOPMED)
A=0.085770 (12025/140200, GnomAD)
A=0.06412 (1812/28258, 14KJPN) (+ 19 more)
A=0.10461 (1976/18890, ALFA)
A=0.06420 (1076/16760, 8.3KJPN)
A=0.0726 (465/6404, 1000G_30x)
A=0.0737 (369/5008, 1000G)
A=0.1596 (715/4480, Estonian)
A=0.1108 (427/3854, ALSPAC)
A=0.1017 (377/3708, TWINSUK)
A=0.0698 (204/2922, KOREAN)
A=0.0737 (135/1832, Korea1K)
A=0.114 (114/998, GoNL)
A=0.105 (63/600, NorthernSweden)
A=0.076 (25/328, HapMap)
A=0.111 (24/216, Qatari)
A=0.060 (13/216, Vietnamese)
G=0.461 (47/102, SGDP_PRJ)
A=0.00 (0/50, Ancient Sardinia)
A=0.12 (5/40, GENOME_DK)
G=0.5 (5/10, Siberian)
A=0.5 (5/10, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNF10 : 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 18890 G=0.89539 A=0.10461
European Sub 14286 G=0.87624 A=0.12376
African Sub 2946 G=0.9752 A=0.0248
African Others Sub 114 G=0.974 A=0.026
African American Sub 2832 G=0.9753 A=0.0247
Asian Sub 112 G=0.929 A=0.071
East Asian Sub 86 G=0.93 A=0.07
Other Asian Sub 26 G=0.92 A=0.08
Latin American 1 Sub 146 G=0.932 A=0.068
Latin American 2 Sub 610 G=0.915 A=0.085
South Asian Sub 98 G=0.91 A=0.09
Other Sub 692 G=0.919 A=0.081


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=0.922392 A=0.077608
gnomAD - Genomes Global Study-wide 140200 G=0.914230 A=0.085770
gnomAD - Genomes European Sub 75908 G=0.88453 A=0.11547
gnomAD - Genomes African Sub 42034 G=0.96926 A=0.03074
gnomAD - Genomes American Sub 13654 G=0.89900 A=0.10100
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9386 A=0.0614
gnomAD - Genomes East Asian Sub 3130 G=0.9307 A=0.0693
gnomAD - Genomes Other Sub 2152 G=0.9219 A=0.0781
14KJPN JAPANESE Study-wide 28258 G=0.93588 A=0.06412
Allele Frequency Aggregator Total Global 18890 G=0.89539 A=0.10461
Allele Frequency Aggregator European Sub 14286 G=0.87624 A=0.12376
Allele Frequency Aggregator African Sub 2946 G=0.9752 A=0.0248
Allele Frequency Aggregator Other Sub 692 G=0.919 A=0.081
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.915 A=0.085
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.932 A=0.068
Allele Frequency Aggregator Asian Sub 112 G=0.929 A=0.071
Allele Frequency Aggregator South Asian Sub 98 G=0.91 A=0.09
8.3KJPN JAPANESE Study-wide 16760 G=0.93580 A=0.06420
1000Genomes_30x Global Study-wide 6404 G=0.9274 A=0.0726
1000Genomes_30x African Sub 1786 G=0.9759 A=0.0241
1000Genomes_30x Europe Sub 1266 G=0.8918 A=0.1082
1000Genomes_30x South Asian Sub 1202 G=0.9118 A=0.0882
1000Genomes_30x East Asian Sub 1170 G=0.9214 A=0.0786
1000Genomes_30x American Sub 980 G=0.911 A=0.089
1000Genomes Global Study-wide 5008 G=0.9263 A=0.0737
1000Genomes African Sub 1322 G=0.9728 A=0.0272
1000Genomes East Asian Sub 1008 G=0.9216 A=0.0784
1000Genomes Europe Sub 1006 G=0.8936 A=0.1064
1000Genomes South Asian Sub 978 G=0.912 A=0.088
1000Genomes American Sub 694 G=0.912 A=0.088
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=0.8892 A=0.1108
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8983 A=0.1017
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9302 A=0.0698
Korean Genome Project KOREAN Study-wide 1832 G=0.9263 A=0.0737
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.886 A=0.114
Northern Sweden ACPOP Study-wide 600 G=0.895 A=0.105
HapMap Global Study-wide 328 G=0.924 A=0.076
HapMap African Sub 120 G=1.000 A=0.000
HapMap American Sub 120 G=0.850 A=0.150
HapMap Asian Sub 88 G=0.92 A=0.08
Qatari Global Study-wide 216 G=0.889 A=0.111
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.940 A=0.060
SGDP_PRJ Global Study-wide 102 G=0.461 A=0.539
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 50 G=1.00 A=0.00
The Danish reference pan genome Danish Study-wide 40 G=0.88 A=0.12
Siberian Global Study-wide 10 G=0.5 A=0.5
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 12 NC_000012.12:g.120576224G>A
GRCh37.p13 chr 12 NC_000012.11:g.121014027G>A
Gene: RNF10, ring finger protein 10 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RNF10 transcript variant 2 NM_001330474.2:c.2374+274…

NM_001330474.2:c.2374+274G>A

 		N/A Intron Variant
RNF10 transcript variant 1 NM_014868.5:c.2359+274G>A N/A Intron Variant
RNF10 transcript variant X1 XM_005254013.3:c.2224+274…

XM_005254013.3:c.2224+274G>A

 		N/A Intron Variant
RNF10 transcript variant X2 XM_017020282.2:c.2209+274…

XM_017020282.2:c.2209+274G>A

 		N/A Intron Variant
RNF10 transcript variant X5 XM_017020283.3:c. N/A Genic Downstream Transcript Variant
RNF10 transcript variant X3 XM_047429937.1:c. N/A Genic Downstream Transcript Variant
RNF10 transcript variant X4 XM_047429938.1:c. N/A Genic Downstream Transcript Variant
RNF10 transcript variant X6 XM_047429939.1:c. N/A Genic Downstream Transcript Variant
RNF10 transcript variant X7 XM_047429940.1:c. N/A Genic Downstream Transcript Variant
RNF10 transcript variant X8 XM_047429941.1:c. N/A Genic Downstream Transcript Variant
RNF10 transcript variant X9 XM_047429942.1: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
GRCh38.p14 chr 12 NC_000012.12:g.120576224= NC_000012.12:g.120576224G>A
GRCh37.p13 chr 12 NC_000012.11:g.121014027= NC_000012.11:g.121014027G>A
RNF10 transcript variant 2 NM_001330474.2:c.2374+274= NM_001330474.2:c.2374+274G>A
RNF10 transcript variant 1 NM_014868.4:c.2359+274= NM_014868.4:c.2359+274G>A
RNF10 transcript variant 1 NM_014868.5:c.2359+274= NM_014868.5:c.2359+274G>A
RNF10 transcript variant X1 XM_005254010.1:c.2434+274= XM_005254010.1:c.2434+274G>A
RNF10 transcript variant X2 XM_005254011.1:c.2374+274= XM_005254011.1:c.2374+274G>A
RNF10 transcript variant X3 XM_005254012.1:c.2359+274= XM_005254012.1:c.2359+274G>A
RNF10 transcript variant X2 XM_005254013.1:c.2224+274= XM_005254013.1:c.2224+274G>A
RNF10 transcript variant X1 XM_005254013.3:c.2224+274= XM_005254013.3:c.2224+274G>A
RNF10 transcript variant X5 XM_005254014.1:c.2218+274= XM_005254014.1:c.2218+274G>A
RNF10 transcript variant X2 XM_017020282.2:c.2209+274= XM_017020282.2:c.2209+274G>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#.

54 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss5003716 Aug 28, 2002 (107)
2 PERLEGEN ss16334250 Feb 28, 2004 (123)
3 CSHL-HAPMAP ss16582313 Feb 27, 2004 (120)
4 PERLEGEN ss24661860 Sep 20, 2004 (123)
5 ABI ss38931441 Mar 15, 2006 (126)
6 AFFY ss65932797 Nov 30, 2006 (127)
7 BUSHMAN ss198771931 Jul 04, 2010 (132)
8 BCM-HGSC-SUB ss208227191 Jul 04, 2010 (132)
9 1000GENOMES ss236113628 Jul 15, 2010 (132)
10 1000GENOMES ss242636656 Jul 15, 2010 (132)
11 GMI ss281572878 May 04, 2012 (137)
12 TISHKOFF ss563447999 Apr 25, 2013 (138)
13 SSMP ss659032316 Apr 25, 2013 (138)
14 EVA-GONL ss990029260 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1078822274 Aug 21, 2014 (142)
16 1000GENOMES ss1346908762 Aug 21, 2014 (142)
17 DDI ss1427074147 Apr 01, 2015 (144)
18 EVA_GENOME_DK ss1576566548 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1629591799 Apr 01, 2015 (144)
20 EVA_DECODE ss1642139126 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1672585832 Apr 01, 2015 (144)
22 WEILL_CORNELL_DGM ss1933384005 Feb 12, 2016 (147)
23 GENOMED ss1967695973 Jul 19, 2016 (147)
24 JJLAB ss2027448382 Sep 14, 2016 (149)
25 USC_VALOUEV ss2155802648 Dec 20, 2016 (150)
26 HUMAN_LONGEVITY ss2193755202 Dec 20, 2016 (150)
27 GRF ss2700162599 Nov 08, 2017 (151)
28 GNOMAD ss2915945509 Nov 08, 2017 (151)
29 SWEGEN ss3010459495 Nov 08, 2017 (151)
30 BIOINF_KMB_FNS_UNIBA ss3027534848 Nov 08, 2017 (151)
31 CSHL ss3350280568 Nov 08, 2017 (151)
32 EGCUT_WGS ss3677760722 Jul 13, 2019 (153)
33 EVA_DECODE ss3694605201 Jul 13, 2019 (153)
34 ACPOP ss3739441935 Jul 13, 2019 (153)
35 EVA ss3751049327 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3816377634 Jul 13, 2019 (153)
37 SGDP_PRJ ss3879253227 Apr 27, 2020 (154)
38 KRGDB ss3928019199 Apr 27, 2020 (154)
39 KOGIC ss3972876572 Apr 27, 2020 (154)
40 EVA ss3985619547 Apr 26, 2021 (155)
41 TOPMED ss4935097810 Apr 26, 2021 (155)
42 TOMMO_GENOMICS ss5208481178 Apr 26, 2021 (155)
43 1000G_HIGH_COVERAGE ss5292474021 Oct 16, 2022 (156)
44 EVA ss5408664927 Oct 16, 2022 (156)
45 HUGCELL_USP ss5487054935 Oct 16, 2022 (156)
46 EVA ss5510863401 Oct 16, 2022 (156)
47 1000G_HIGH_COVERAGE ss5590811518 Oct 16, 2022 (156)
48 SANFORD_IMAGENETICS ss5654089046 Oct 16, 2022 (156)
49 TOMMO_GENOMICS ss5758900735 Oct 16, 2022 (156)
50 YY_MCH ss5813704690 Oct 16, 2022 (156)
51 EVA ss5838607317 Oct 16, 2022 (156)
52 EVA ss5850576779 Oct 16, 2022 (156)
53 EVA ss5906297826 Oct 16, 2022 (156)
54 EVA ss5945503901 Oct 16, 2022 (156)
55 1000Genomes NC_000012.11 - 121014027 Oct 12, 2018 (152)
56 1000Genomes_30x NC_000012.12 - 120576224 Oct 16, 2022 (156)
57 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 121014027 Oct 12, 2018 (152)
58 Genetic variation in the Estonian population NC_000012.11 - 121014027 Oct 12, 2018 (152)
59 The Danish reference pan genome NC_000012.11 - 121014027 Apr 27, 2020 (154)
60 gnomAD - Genomes NC_000012.12 - 120576224 Apr 26, 2021 (155)
61 Genome of the Netherlands Release 5 NC_000012.11 - 121014027 Apr 27, 2020 (154)
62 HapMap NC_000012.12 - 120576224 Apr 27, 2020 (154)
63 KOREAN population from KRGDB NC_000012.11 - 121014027 Apr 27, 2020 (154)
64 Korean Genome Project NC_000012.12 - 120576224 Apr 27, 2020 (154)
65 Northern Sweden NC_000012.11 - 121014027 Jul 13, 2019 (153)
66 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000012.11 - 121014027 Apr 26, 2021 (155)
67 Qatari NC_000012.11 - 121014027 Apr 27, 2020 (154)
68 SGDP_PRJ NC_000012.11 - 121014027 Apr 27, 2020 (154)
69 Siberian NC_000012.11 - 121014027 Apr 27, 2020 (154)
70 8.3KJPN NC_000012.11 - 121014027 Apr 26, 2021 (155)
71 14KJPN NC_000012.12 - 120576224 Oct 16, 2022 (156)
72 TopMed NC_000012.12 - 120576224 Apr 26, 2021 (155)
73 UK 10K study - Twins NC_000012.11 - 121014027 Oct 12, 2018 (152)
74 A Vietnamese Genetic Variation Database NC_000012.11 - 121014027 Jul 13, 2019 (153)
75 ALFA NC_000012.12 - 120576224 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)
rs11565323 Sep 24, 2004 (123)
rs17584552 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss198771931, ss208227191, ss281572878, ss1642139126 NC_000012.10:119498409:G:A NC_000012.12:120576223:G:A (self)
59729551, 33177639, 23498970, 3154216, 14795626, 35196593, 12726800, 845474, 15425935, 31270207, 8319002, 66450485, 33177639, 7359307, ss236113628, ss242636656, ss563447999, ss659032316, ss990029260, ss1078822274, ss1346908762, ss1427074147, ss1576566548, ss1629591799, ss1672585832, ss1933384005, ss1967695973, ss2027448382, ss2155802648, ss2700162599, ss2915945509, ss3010459495, ss3350280568, ss3677760722, ss3739441935, ss3751049327, ss3879253227, ss3928019199, ss3985619547, ss5208481178, ss5408664927, ss5510863401, ss5654089046, ss5838607317, ss5945503901 NC_000012.11:121014026:G:A NC_000012.12:120576223:G:A (self)
78337453, 421304774, 918702, 29254573, 92737839, 150643467, 13280587749, ss2193755202, ss3027534848, ss3694605201, ss3816377634, ss3972876572, ss4935097810, ss5292474021, ss5487054935, ss5590811518, ss5758900735, ss5813704690, ss5850576779, ss5906297826 NC_000012.12:120576223:G:A NC_000012.12:120576223:G:A (self)
ss16582313 NT_009775.14:11532768:G:A NC_000012.12:120576223:G:A (self)
ss5003716, ss16334250, ss24661860, ss38931441, ss65932797 NT_009775.17:11590556:G:A NC_000012.12:120576223: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 rs3817301

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