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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.

rs7332962

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:24887091 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.075133 (19887/264690, TOPMED)
T=0.003752 (674/179644, ALFA)
T=0.10823 (8518/78700, PAGE_STUDY) (+ 8 more)
T=0.0759 (486/6404, 1000G_30x)
T=0.0737 (369/5008, 1000G)
T=0.0005 (2/3854, ALSPAC)
T=0.0013 (5/3708, TWINSUK)
T=0.001 (1/998, GoNL)
T=0.117 (36/308, HapMap)
T=0.051 (11/216, Qatari)
C=0.42 (16/38, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CENPJ : Intron Variant
RNF17 : 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 179766 C=0.996228 A=0.000000, G=0.000000, T=0.003772
European Sub 157524 C=0.999041 A=0.000000, G=0.000000, T=0.000959
African Sub 3396 C=0.8834 A=0.0000, G=0.0000, T=0.1166
African Others Sub 128 C=0.883 A=0.000, G=0.000, T=0.117
African American Sub 3268 C=0.8834 A=0.0000, G=0.0000, T=0.1166
Asian Sub 6308 C=0.9998 A=0.0000, G=0.0000, T=0.0002
East Asian Sub 4488 C=1.0000 A=0.0000, G=0.0000, T=0.0000
Other Asian Sub 1820 C=0.9995 A=0.0000, G=0.0000, T=0.0005
Latin American 1 Sub 450 C=0.964 A=0.000, G=0.000, T=0.036
Latin American 2 Sub 1026 C=0.9951 A=0.0000, G=0.0000, T=0.0049
South Asian Sub 296 C=1.000 A=0.000, G=0.000, T=0.000
Other Sub 10766 C=0.98988 A=0.00000, G=0.00000, T=0.01012


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 C=0.924867 T=0.075133
Allele Frequency Aggregator Total Global 179644 C=0.996248 A=0.000000, G=0.000000, T=0.003752
Allele Frequency Aggregator European Sub 157420 C=0.999041 A=0.000000, G=0.000000, T=0.000959
Allele Frequency Aggregator Other Sub 10762 C=0.98987 A=0.00000, G=0.00000, T=0.01013
Allele Frequency Aggregator Asian Sub 6308 C=0.9998 A=0.0000, G=0.0000, T=0.0002
Allele Frequency Aggregator African Sub 3382 C=0.8841 A=0.0000, G=0.0000, T=0.1159
Allele Frequency Aggregator Latin American 2 Sub 1026 C=0.9951 A=0.0000, G=0.0000, T=0.0049
Allele Frequency Aggregator Latin American 1 Sub 450 C=0.964 A=0.000, G=0.000, T=0.036
Allele Frequency Aggregator South Asian Sub 296 C=1.000 A=0.000, G=0.000, T=0.000
The PAGE Study Global Study-wide 78700 C=0.89177 T=0.10823
The PAGE Study AfricanAmerican Sub 32516 C=0.78229 T=0.21771
The PAGE Study Mexican Sub 10810 C=0.98751 T=0.01249
The PAGE Study Asian Sub 8318 C=0.9999 T=0.0001
The PAGE Study PuertoRican Sub 7918 C=0.9350 T=0.0650
The PAGE Study NativeHawaiian Sub 4534 C=0.9980 T=0.0020
The PAGE Study Cuban Sub 4228 C=0.9600 T=0.0400
The PAGE Study Dominican Sub 3828 C=0.8892 T=0.1108
The PAGE Study CentralAmerican Sub 2450 C=0.9580 T=0.0420
The PAGE Study SouthAmerican Sub 1982 C=0.9783 T=0.0217
The PAGE Study NativeAmerican Sub 1260 C=0.9690 T=0.0310
The PAGE Study SouthAsian Sub 856 C=0.999 T=0.001
1000Genomes_30x Global Study-wide 6404 C=0.9241 T=0.0759
1000Genomes_30x African Sub 1786 C=0.7424 T=0.2576
1000Genomes_30x Europe Sub 1266 C=0.9976 T=0.0024
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=0.977 T=0.023
1000Genomes Global Study-wide 5008 C=0.9263 T=0.0737
1000Genomes African Sub 1322 C=0.7345 T=0.2655
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9980 T=0.0020
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.977 T=0.023
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9995 T=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9987 T=0.0013
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.999 T=0.001
HapMap Global Study-wide 308 C=0.883 T=0.117
HapMap African Sub 112 C=0.679 T=0.321
HapMap American Sub 110 C=1.000 T=0.000
HapMap Asian Sub 86 C=1.00 T=0.00
Qatari Global Study-wide 216 C=0.949 T=0.051
SGDP_PRJ Global Study-wide 38 C=0.42 T=0.58
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 13 NC_000013.11:g.24887091C>A
GRCh38.p14 chr 13 NC_000013.11:g.24887091C>G
GRCh38.p14 chr 13 NC_000013.11:g.24887091C>T
GRCh37.p13 chr 13 NC_000013.10:g.25461229C>A
GRCh37.p13 chr 13 NC_000013.10:g.25461229C>G
GRCh37.p13 chr 13 NC_000013.10:g.25461229C>T
CENPJ RefSeqGene NG_009165.2:g.40857G>T
CENPJ RefSeqGene NG_009165.2:g.40857G>C
CENPJ RefSeqGene NG_009165.2:g.40857G>A
Gene: CENPJ, centromere protein J (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CENPJ transcript variant 1 NM_018451.5:c.3302-1421G>T N/A Intron Variant
CENPJ transcript variant 2 NR_047594.2:n. N/A Intron Variant
CENPJ transcript variant 3 NR_047595.2:n. N/A Intron Variant
CENPJ transcript variant X4 XM_011535149.3:c.3302-706…

XM_011535149.3:c.3302-706G>T

 		N/A Intron Variant
CENPJ transcript variant X1 XM_047430482.1:c.3302-142…

XM_047430482.1:c.3302-1421G>T

 		N/A Intron Variant
CENPJ transcript variant X1 XM_047430483.1:c.3302-142…

XM_047430483.1:c.3302-1421G>T

 		N/A Intron Variant
CENPJ transcript variant X3 XM_047430484.1:c.3302-706…

XM_047430484.1:c.3302-706G>T

 		N/A Intron Variant
CENPJ transcript variant X5 XM_011535150.3:c. N/A Genic Downstream Transcript Variant
CENPJ transcript variant X7 XM_017020673.2:c. N/A Genic Downstream Transcript Variant
CENPJ transcript variant X8 XM_047430485.1:c. N/A Genic Downstream Transcript Variant
CENPJ transcript variant X2 XR_941627.2:n. N/A Intron Variant
CENPJ transcript variant X6 XR_941628.2:n. N/A Genic Downstream Transcript Variant
Gene: RNF17, ring finger protein 17 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RNF17 transcript variant 2 NM_001184993.2:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant 1 NM_031277.3:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X2 XM_011535156.3:c.*11-1023…

XM_011535156.3:c.*11-1023C>A

 		N/A Intron Variant
RNF17 transcript variant X5 XM_006719846.4:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X6 XM_006719849.3:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X1 XM_011535152.3:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X3 XM_011535155.3:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X4 XM_011535157.3:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X7 XM_011535158.3:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X8 XM_011535159.3:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X9 XM_011535160.3:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X12 XM_011535162.2:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X13 XM_011535163.2:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X14 XM_011535164.3:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X10 XM_017020676.2:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X15 XM_047430486.1:c. N/A Genic Downstream Transcript Variant
RNF17 transcript variant X11 XM_047430488.1: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 C= A G T
GRCh38.p14 chr 13 NC_000013.11:g.24887091= NC_000013.11:g.24887091C>A NC_000013.11:g.24887091C>G NC_000013.11:g.24887091C>T
GRCh37.p13 chr 13 NC_000013.10:g.25461229= NC_000013.10:g.25461229C>A NC_000013.10:g.25461229C>G NC_000013.10:g.25461229C>T
CENPJ RefSeqGene NG_009165.2:g.40857= NG_009165.2:g.40857G>T NG_009165.2:g.40857G>C NG_009165.2:g.40857G>A
CENPJ transcript variant 1 NM_018451.4:c.3302-1421= NM_018451.4:c.3302-1421G>T NM_018451.4:c.3302-1421G>C NM_018451.4:c.3302-1421G>A
CENPJ transcript variant 1 NM_018451.5:c.3302-1421= NM_018451.5:c.3302-1421G>T NM_018451.5:c.3302-1421G>C NM_018451.5:c.3302-1421G>A
CENPJ transcript variant X4 XM_011535149.3:c.3302-706= XM_011535149.3:c.3302-706G>T XM_011535149.3:c.3302-706G>C XM_011535149.3:c.3302-706G>A
RNF17 transcript variant X2 XM_011535156.3:c.*11-1023= XM_011535156.3:c.*11-1023C>A XM_011535156.3:c.*11-1023C>G XM_011535156.3:c.*11-1023C>T
CENPJ transcript variant X1 XM_047430482.1:c.3302-1421= XM_047430482.1:c.3302-1421G>T XM_047430482.1:c.3302-1421G>C XM_047430482.1:c.3302-1421G>A
CENPJ transcript variant X1 XM_047430483.1:c.3302-1421= XM_047430483.1:c.3302-1421G>T XM_047430483.1:c.3302-1421G>C XM_047430483.1:c.3302-1421G>A
CENPJ transcript variant X3 XM_047430484.1:c.3302-706= XM_047430484.1:c.3302-706G>T XM_047430484.1:c.3302-706G>C XM_047430484.1:c.3302-706G>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#.

63 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss11087135 Jul 11, 2003 (116)
2 1000GENOMES ss114423959 Jan 25, 2009 (130)
3 ILLUMINA-UK ss118390256 Feb 14, 2009 (130)
4 COMPLETE_GENOMICS ss168983070 Jul 04, 2010 (132)
5 BUSHMAN ss198977726 Jul 04, 2010 (132)
6 1000GENOMES ss226082225 Jul 14, 2010 (132)
7 ILLUMINA ss481206929 May 04, 2012 (137)
8 ILLUMINA ss483168597 May 04, 2012 (137)
9 EXOME_CHIP ss491477255 May 04, 2012 (137)
10 ILLUMINA ss534192287 Sep 08, 2015 (146)
11 TISHKOFF ss563552629 Apr 25, 2013 (138)
12 ILLUMINA ss779263850 Sep 08, 2015 (146)
13 ILLUMINA ss780801831 Sep 08, 2015 (146)
14 ILLUMINA ss781423475 Sep 08, 2015 (146)
15 ILLUMINA ss783483254 Sep 08, 2015 (146)
16 ILLUMINA ss834730538 Sep 08, 2015 (146)
17 EVA-GONL ss990196896 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1078940572 Aug 21, 2014 (142)
19 1000GENOMES ss1347508600 Aug 21, 2014 (142)
20 EVA_UK10K_ALSPAC ss1629896898 Apr 01, 2015 (144)
21 EVA_DECODE ss1642302324 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1672890931 Apr 01, 2015 (144)
23 ILLUMINA ss1752097977 Sep 08, 2015 (146)
24 ILLUMINA ss1917881862 Feb 12, 2016 (147)
25 WEILL_CORNELL_DGM ss1933565327 Feb 12, 2016 (147)
26 ILLUMINA ss1946356565 Feb 12, 2016 (147)
27 ILLUMINA ss1959487449 Feb 12, 2016 (147)
28 HUMAN_LONGEVITY ss2194882227 Dec 20, 2016 (150)
29 ILLUMINA ss2633039858 Nov 08, 2017 (151)
30 ILLUMINA ss2633039859 Nov 08, 2017 (151)
31 GNOMAD ss2917637810 Nov 08, 2017 (151)
32 AFFY ss2984999126 Nov 08, 2017 (151)
33 AFFY ss2985633821 Nov 08, 2017 (151)
34 ILLUMINA ss3021491602 Nov 08, 2017 (151)
35 ILLUMINA ss3627022733 Oct 12, 2018 (152)
36 ILLUMINA ss3627022734 Oct 12, 2018 (152)
37 ILLUMINA ss3631044325 Oct 12, 2018 (152)
38 ILLUMINA ss3634535929 Oct 12, 2018 (152)
39 ILLUMINA ss3640243260 Oct 12, 2018 (152)
40 ILLUMINA ss3644609589 Oct 12, 2018 (152)
41 ILLUMINA ss3651876552 Oct 12, 2018 (152)
42 ILLUMINA ss3653769485 Oct 12, 2018 (152)
43 EVA_DECODE ss3694933374 Jul 13, 2019 (153)
44 ILLUMINA ss3725379019 Jul 13, 2019 (153)
45 ILLUMINA ss3744404282 Jul 13, 2019 (153)
46 ILLUMINA ss3744836672 Jul 13, 2019 (153)
47 PAGE_CC ss3771734664 Jul 13, 2019 (153)
48 ILLUMINA ss3772335794 Jul 13, 2019 (153)
49 KHV_HUMAN_GENOMES ss3816571436 Jul 13, 2019 (153)
50 SGDP_PRJ ss3879601116 Apr 27, 2020 (154)
51 TOPMED ss4940063088 Apr 26, 2021 (155)
52 1000G_HIGH_COVERAGE ss5293109281 Oct 16, 2022 (156)
53 EVA ss5409629528 Oct 16, 2022 (156)
54 HUGCELL_USP ss5487534573 Oct 16, 2022 (156)
55 EVA ss5510909213 Oct 16, 2022 (156)
56 1000G_HIGH_COVERAGE ss5591749532 Oct 16, 2022 (156)
57 SANFORD_IMAGENETICS ss5624319281 Oct 16, 2022 (156)
58 SANFORD_IMAGENETICS ss5654408772 Oct 16, 2022 (156)
59 EVA ss5839226981 Oct 16, 2022 (156)
60 EVA ss5847692333 Oct 16, 2022 (156)
61 EVA ss5924384131 Oct 16, 2022 (156)
62 EVA ss5945813638 Oct 16, 2022 (156)
63 EVA ss5979412345 Oct 16, 2022 (156)
64 1000Genomes NC_000013.10 - 25461229 Oct 12, 2018 (152)
65 1000Genomes_30x NC_000013.11 - 24887091 Oct 16, 2022 (156)
66 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 25461229 Oct 12, 2018 (152)
67 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 425606770 (NC_000013.11:24887090:C:A 1/139998)
Row 425606771 (NC_000013.11:24887090:C:T 10092/139964)

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

Submission ignored due to conflicting rows:
Row 425606770 (NC_000013.11:24887090:C:A 1/139998)
Row 425606771 (NC_000013.11:24887090:C:T 10092/139964)

- Apr 26, 2021 (155)
69 Genome of the Netherlands Release 5 NC_000013.10 - 25461229 Apr 27, 2020 (154)
70 HapMap NC_000013.11 - 24887091 Apr 27, 2020 (154)
71 The PAGE Study NC_000013.11 - 24887091 Jul 13, 2019 (153)
72 Qatari NC_000013.10 - 25461229 Apr 27, 2020 (154)
73 SGDP_PRJ NC_000013.10 - 25461229 Apr 27, 2020 (154)
74 TopMed NC_000013.11 - 24887091 Apr 26, 2021 (155)
75 UK 10K study - Twins NC_000013.10 - 25461229 Oct 12, 2018 (152)
76 ALFA NC_000013.11 - 24887091 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
3329944240 NC_000013.11:24887090:C:A NC_000013.11:24887090:C:A (self)
3329944240 NC_000013.11:24887090:C:G NC_000013.11:24887090:C:G (self)
ss114423959, ss118390256, ss168983070, ss198977726, ss483168597, ss1642302324 NC_000013.9:24359228:C:T NC_000013.11:24887090:C:T (self)
60352545, 33517171, 14954287, 15607257, 31618096, 33517171, ss226082225, ss481206929, ss491477255, ss534192287, ss563552629, ss779263850, ss780801831, ss781423475, ss783483254, ss834730538, ss990196896, ss1078940572, ss1347508600, ss1629896898, ss1672890931, ss1752097977, ss1917881862, ss1933565327, ss1946356565, ss1959487449, ss2633039858, ss2633039859, ss2917637810, ss2984999126, ss2985633821, ss3021491602, ss3627022733, ss3627022734, ss3631044325, ss3634535929, ss3640243260, ss3644609589, ss3651876552, ss3653769485, ss3744404282, ss3744836672, ss3772335794, ss3879601116, ss5409629528, ss5510909213, ss5624319281, ss5654408772, ss5839226981, ss5847692333, ss5945813638, ss5979412345 NC_000013.10:25461228:C:T NC_000013.11:24887090:C:T (self)
79275467, 948828, 956133, 155608746, 3329944240, ss2194882227, ss3694933374, ss3725379019, ss3771734664, ss3816571436, ss4940063088, ss5293109281, ss5487534573, ss5591749532, ss5924384131 NC_000013.11:24887090:C:T NC_000013.11:24887090:C:T (self)
ss11087135 NT_009799.12:6441228:C:T NC_000013.11:24887090:C: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 rs7332962

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