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dbSNP Short Genetic Variations

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.

rs10894604

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr11:132771851 (GRCh38.p12) 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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.25362 (31846/125568, TOPMED)
G=0.2525 (7812/30940, GnomAD)
G=0.151 (755/5008, 1000G) (+ 3 more)
G=0.304 (1362/4480, Estonian)
G=0.358 (1378/3854, ALSPAC)
G=0.354 (1311/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OPCML : 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.p12 chr 11 NC_000011.10:g.132771851T>G
GRCh37.p13 chr 11 NC_000011.9:g.132641746T>G
OPCML RefSeqGene NG_012107.1:g.765658A>C
Gene: OPCML, opioid binding protein/cell adhesion molecule like (minus strand)
Molecule type Change Amino acid[Codon] SO Term
OPCML transcript variant 2 NM_001012393.2:c. N/A Intron Variant
OPCML transcript variant 3 NM_001319103.1:c. N/A Intron Variant
OPCML transcript variant 4 NM_001319104.1:c. N/A Intron Variant
OPCML transcript variant 5 NM_001319105.1:c. N/A Intron Variant
OPCML transcript variant 6 NM_001319106.1:c. N/A Intron Variant
OPCML transcript variant 1 NM_002545.4:c. N/A Intron Variant
OPCML transcript variant X1 XM_006718846.3:c. N/A Intron Variant
OPCML transcript variant X2 XM_011542856.3:c. 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
TopMed Global Study-wide 125568 T=0.74638 G=0.25362
gnomAD - Genomes Global Study-wide 30940 T=0.7475 G=0.2525
gnomAD - Genomes European Sub 18484 T=0.6842 G=0.3158
gnomAD - Genomes African Sub 8712 T=0.841 G=0.159
gnomAD - Genomes East Asian Sub 1622 T=0.967 G=0.033
gnomAD - Genomes Other Sub 982 T=0.73 G=0.27
gnomAD - Genomes American Sub 838 T=0.77 G=0.23
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.75 G=0.25
1000Genomes Global Study-wide 5008 T=0.849 G=0.151
1000Genomes African Sub 1322 T=0.887 G=0.113
1000Genomes East Asian Sub 1008 T=0.973 G=0.027
1000Genomes Europe Sub 1006 T=0.698 G=0.302
1000Genomes South Asian Sub 978 T=0.87 G=0.13
1000Genomes American Sub 694 T=0.79 G=0.21
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.696 G=0.304
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.642 G=0.358
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.646 G=0.354
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 T= G Note
GRCh38.p12 chr 11 NC_000011.10:g.132771851T= NC_000011.10:g.13277185...

NC_000011.10:g.132771851T>G

GRCh37.p13 chr 11 NC_000011.9:g.132641746T= NC_000011.9:g.132641746T>G
OPCML RefSeqGene NG_012107.1:g.765658A= NG_012107.1:g.765658A>C
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, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15980365 Feb 27, 2004 (120)
2 SC_SNP ss18708288 Feb 27, 2004 (120)
3 SC_SNP ss18935436 Feb 27, 2004 (120)
4 AFFY ss76597337 Dec 06, 2007 (129)
5 BCMHGSC_JDW ss88890995 Mar 24, 2008 (129)
6 KRIBB_YJKIM ss105017112 Feb 05, 2009 (130)
7 1000GENOMES ss111316163 Jan 25, 2009 (130)
8 ENSEMBL ss132936313 Dec 01, 2009 (131)
9 BUSHMAN ss203411155 Jul 04, 2010 (132)
10 1000GENOMES ss211222106 Jul 14, 2010 (132)
11 1000GENOMES ss225549788 Jul 14, 2010 (132)
12 1000GENOMES ss235781662 Jul 15, 2010 (132)
13 GMI ss281231607 May 04, 2012 (137)
14 GMI ss286485749 Apr 25, 2013 (138)
15 PJP ss291172717 May 09, 2011 (134)
16 TISHKOFF ss562927522 Apr 25, 2013 (138)
17 SSMP ss658451000 Apr 25, 2013 (138)
18 EVA-GONL ss989128723 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1078169576 Aug 21, 2014 (142)
20 1000GENOMES ss1343594766 Aug 21, 2014 (142)
21 DDI ss1426809623 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1576050378 Apr 01, 2015 (144)
23 EVA_DECODE ss1598799609 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1627805875 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1670799908 Apr 01, 2015 (144)
26 EVA_SVP ss1713298364 Apr 01, 2015 (144)
27 WEILL_CORNELL_DGM ss1932486917 Feb 12, 2016 (147)
28 JJLAB ss2026990953 Sep 14, 2016 (149)
29 USC_VALOUEV ss2155308168 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2186996301 Dec 20, 2016 (150)
31 TOPMED ss2350594662 Dec 20, 2016 (150)
32 SYSTEMSBIOZJU ss2627972147 Nov 08, 2017 (151)
33 GRF ss2699624163 Nov 08, 2017 (151)
34 GNOMAD ss2906196889 Nov 08, 2017 (151)
35 AFFY ss2984963273 Nov 08, 2017 (151)
36 AFFY ss2985605321 Nov 08, 2017 (151)
37 SWEGEN ss3009031565 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3027298004 Nov 08, 2017 (151)
39 TOPMED ss3160372906 Nov 08, 2017 (151)
40 CSHL ss3349868559 Nov 08, 2017 (151)
41 ILLUMINA ss3653735479 Oct 12, 2018 (152)
42 1000Genomes NC_000011.9 - 132641746 Oct 12, 2018 (152)
43 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 132641746 Oct 12, 2018 (152)
44 Genetic variation in the Estonian population NC_000011.9 - 132641746 Oct 12, 2018 (152)
45 gnomAD - Genomes NC_000011.9 - 132641746 Oct 12, 2018 (152)
46 TopMed NC_000011.10 - 132771851 Oct 12, 2018 (152)
47 UK 10K study - Twins NC_000011.9 - 132641746 Oct 12, 2018 (152)
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
ss88890995, ss111316163, ss203411155, ss211222106, ss281231607, ss286485749, ss291172717, ss1598799609, ss1713298364 NC_000011.8:132146955:T:G NC_000011.10:132771850:T:G (self)
56198993, 31208283, 22103504, 39898411, 31208283, ss225549788, ss235781662, ss562927522, ss658451000, ss989128723, ss1078169576, ss1343594766, ss1426809623, ss1576050378, ss1627805875, ss1670799908, ss1932486917, ss2026990953, ss2155308168, ss2350594662, ss2627972147, ss2699624163, ss2906196889, ss2984963273, ss2985605321, ss3009031565, ss3349868559, ss3653735479 NC_000011.9:132641745:T:G NC_000011.10:132771850:T:G (self)
75735822, ss2186996301, ss3027298004, ss3160372906 NC_000011.10:132771850:T:G NC_000011.10:132771850:T:G (self)
ss15980365, ss18708288, ss18935436 NT_033899.6:36185532:T:G NC_000011.10:132771850:T:G (self)
ss76597337, ss105017112, ss132936313 NT_033899.8:36204161:T:G NC_000011.10:132771850:T:G (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 rs10894604

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.post104+4a6ee9c