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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs12287931

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr11:100005490 (GRCh38.p7) 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=0.37846 (47522/125568, TOPMED)
A=0.3674 (11343/30874, GnomAD)
A=0.340 (1705/5008, 1000G) (+ 2 more)
A=0.299 (1151/3854, ALSPAC)
A=0.300 (1111/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CNTN5 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p7 chr 11 NC_000011.10:g.100005490G>A
GRCh37.p13 chr 11 NC_000011.9:g.99876222G>A
Gene: CNTN5, contactin 5 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CNTN5 transcript variant 2 NM_001243270.1:c. N/A Intron Variant
CNTN5 transcript variant 4 NM_001243271.1:c. N/A Intron Variant
CNTN5 transcript variant 1 NM_014361.3:c. N/A Intron Variant
CNTN5 transcript variant 3 NM_175566.2:c. N/A Intron Variant
CNTN5 transcript variant X2 XM_011542871.1:c. N/A Intron Variant
CNTN5 transcript variant X3 XM_011542873.1:c. N/A Intron Variant
CNTN5 transcript variant X1 XM_017017926.1:c. N/A Intron Variant
CNTN5 transcript variant X4 XM_017017927.1:c. N/A Intron Variant
CNTN5 transcript variant X5 XM_017017928.1:c. N/A Intron Variant
CNTN5 transcript variant X7 XM_017017929.1:c. N/A Intron Variant
CNTN5 transcript variant X6 XR_001747909.1: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

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
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.62154 A=0.37846
The Genome Aggregation Database Global Study-wide 30874 G=0.6326 A=0.3674
The Genome Aggregation Database European Sub 18448 G=0.7021 A=0.2979
The Genome Aggregation Database African Sub 8698 G=0.424 A=0.576
The Genome Aggregation Database East Asian Sub 1612 G=0.880 A=0.120
The Genome Aggregation Database Other Sub 980 G=0.70 A=0.30
The Genome Aggregation Database American Sub 834 G=0.73 A=0.27
The Genome Aggregation Database Ashkenazi Jewish Sub 302 G=0.59 A=0.41
1000Genomes Global Study-wide 5008 G=0.660 A=0.340
1000Genomes African Sub 1322 G=0.393 A=0.607
1000Genomes East Asian Sub 1008 G=0.883 A=0.117
1000Genomes Europe Sub 1006 G=0.685 A=0.315
1000Genomes South Asian Sub 978 G=0.72 A=0.28
1000Genomes American Sub 694 G=0.72 A=0.28
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.701 A=0.299
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.700 A=0.300
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 Note
GRCh38.p7 chr 11 NC_000011.10:g.100005490G= NC_000011.10:g.10000549...

NC_000011.10:g.100005490G>A

GRCh37.p13 chr 11 NC_000011.9:g.99876222G= NC_000011.9:g.99876222G>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#.

41 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18715462 Feb 28, 2004 (120)
2 HGSV ss79704315 Dec 15, 2007 (130)
3 HGSV ss83282685 Dec 15, 2007 (130)
4 BCMHGSC_JDW ss88736881 Mar 24, 2008 (129)
5 HUMANGENOME_JCVI ss97504748 Feb 04, 2009 (130)
6 1000GENOMES ss115054492 Jan 25, 2009 (130)
7 ILLUMINA-UK ss119944760 Dec 01, 2009 (131)
8 ENSEMBL ss132769894 Dec 01, 2009 (131)
9 ENSEMBL ss143021491 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss168712146 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss170735332 Jul 04, 2010 (132)
12 BUSHMAN ss203110975 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss207696580 Jul 04, 2010 (132)
14 1000GENOMES ss225418998 Jul 14, 2010 (132)
15 1000GENOMES ss235687163 Jul 15, 2010 (132)
16 1000GENOMES ss242292161 Jul 15, 2010 (132)
17 PJP ss291122400 May 09, 2011 (134)
18 GMI ss475774430 May 04, 2012 (137)
19 TISHKOFF ss562774772 Apr 25, 2013 (138)
20 SSMP ss658296124 Apr 25, 2013 (138)
21 EVA-GONL ss988878099 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1077982750 Aug 21, 2014 (142)
23 1000GENOMES ss1342645449 Aug 21, 2014 (142)
24 DDI ss1426735919 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1575903210 Apr 01, 2015 (144)
26 EVA_DECODE ss1598541662 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1627290703 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1670284736 Apr 01, 2015 (144)
29 HAMMER_LAB ss1806961501 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1932240991 Feb 12, 2016 (147)
31 GENOMED ss1967437914 Jul 19, 2016 (147)
32 JJLAB ss2026863902 Sep 14, 2016 (149)
33 USC_VALOUEV ss2155176013 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2185039341 Dec 20, 2016 (150)
35 TOPMED ss2348618572 Dec 20, 2016 (150)
36 GRF ss2699479797 Nov 08, 2017 (151)
37 GNOMAD ss2903549111 Nov 08, 2017 (151)
38 SWEGEN ss3008651872 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3027230137 Nov 08, 2017 (151)
40 TOPMED ss3154307311 Nov 08, 2017 (151)
41 CSHL ss3349757101 Nov 08, 2017 (151)
42 1000Genomes NC_000011.9 - 99876222 Jul 20, 2018 (151)
43 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 99876222 Jul 20, 2018 (151)
44 The Genome Aggregation Database NC_000011.9 - 99876222 Jul 20, 2018 (151)
45 Trans-Omics for Precision Medicine NC_000011.10 - 100005490 Jul 20, 2018 (151)
46 UK 10K study - Twins NC_000011.9 - 99876222 Jul 20, 2018 (151)
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)
rs58270101 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss79704315, ss83282685, ss88736881, ss115054492, ss119944760, ss168712146, ss170735332, ss203110975, ss207696580, ss291122400, ss475774430, ss1598541662 NC_000011.8:99381431:G= NC_000011.10:100005489:G= (self)
55215538, 30642952, 37250633, 30642952, ss225418998, ss235687163, ss242292161, ss562774772, ss658296124, ss988878099, ss1077982750, ss1342645449, ss1426735919, ss1575903210, ss1627290703, ss1670284736, ss1806961501, ss1932240991, ss1967437914, ss2026863902, ss2155176013, ss2348618572, ss2699479797, ss2903549111, ss3008651872, ss3349757101 NC_000011.9:99876221:G= NC_000011.10:100005489:G= (self)
70670730, ss2185039341, ss3027230137, ss3154307311 NC_000011.10:100005489:G= NC_000011.10:100005489:G= (self)
ss18715462 NT_033899.6:3420073:G= NC_000011.10:100005489:G= (self)
ss97504748, ss132769894, ss143021491 NT_033899.8:3438637:G= NC_000011.10:100005489:G= (self)
ss79704315, ss83282685, ss88736881, ss115054492, ss119944760, ss168712146, ss170735332, ss203110975, ss207696580, ss291122400, ss475774430, ss1598541662 NC_000011.8:99381431:G>A NC_000011.10:100005489:G>A (self)
55215538, 30642952, 37250633, 30642952, ss225418998, ss235687163, ss242292161, ss562774772, ss658296124, ss988878099, ss1077982750, ss1342645449, ss1426735919, ss1575903210, ss1627290703, ss1670284736, ss1806961501, ss1932240991, ss1967437914, ss2026863902, ss2155176013, ss2348618572, ss2699479797, ss2903549111, ss3008651872, ss3349757101 NC_000011.9:99876221:G>A NC_000011.10:100005489:G>A (self)
70670730, ss2185039341, ss3027230137, ss3154307311 NC_000011.10:100005489:G>A NC_000011.10:100005489:G>A (self)
ss18715462 NT_033899.6:3420073:G>A NC_000011.10:100005489:G>A (self)
ss97504748, ss132769894, ss143021491 NT_033899.8:3438637:G>A NC_000011.10:100005489: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 rs12287931

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: 0.1.4.post833+d3ba21e