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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.

rs10190105

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr2:47254502 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.18673 (23447/125568, TOPMED)
G=0.2017 (6233/30902, GnomAD)
G=0.241 (1206/5008, 1000G) (+ 3 more)
G=0.225 (1009/4480, Estonian)
G=0.195 (752/3854, ALSPAC)
G=0.200 (742/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC101927043 : Intron Variant
LOC107985882 : 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 2 NC_000002.12:g.47254502A>G
GRCh37.p13 chr 2 NC_000002.11:g.47481641A>G
Gene: LOC101927043, uncharacterized LOC101927043 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
EPCAM-DT transcript variant 1 NR_110207.1:n. N/A Intron Variant
EPCAM-DT transcript variant 2 NR_110208.1:n. N/A Intron Variant
Gene: LOC107985882, uncharacterized LOC107985882 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107985882 transcript XR_001739451.1: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
TopMed Global Study-wide 125568 A=0.81327 G=0.18673
gnomAD - Genomes Global Study-wide 30902 A=0.7983 G=0.2017
gnomAD - Genomes European Sub 18444 A=0.7881 G=0.2119
gnomAD - Genomes African Sub 8722 A=0.881 G=0.119
gnomAD - Genomes East Asian Sub 1618 A=0.438 G=0.562
gnomAD - Genomes Other Sub 980 A=0.81 G=0.19
gnomAD - Genomes American Sub 836 A=0.80 G=0.20
gnomAD - Genomes Ashkenazi Jewish Sub 302 A=0.90 G=0.10
1000Genomes Global Study-wide 5008 A=0.759 G=0.241
1000Genomes African Sub 1322 A=0.924 G=0.076
1000Genomes East Asian Sub 1008 A=0.453 G=0.547
1000Genomes Europe Sub 1006 A=0.813 G=0.187
1000Genomes South Asian Sub 978 A=0.77 G=0.23
1000Genomes American Sub 694 A=0.80 G=0.20
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.775 G=0.225
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.805 G=0.195
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.800 G=0.200
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 A= G Note
GRCh38.p12 chr 2 NC_000002.12:g.47254502A= NC_000002.12:g.47254502A>G
GRCh37.p13 chr 2 NC_000002.11:g.47481641A= NC_000002.11:g.47481641A>G
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#.

30 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 WUGSC_SSAHASNP ss14054205 Dec 05, 2003 (119)
2 HGSV ss78385671 Dec 07, 2007 (129)
3 BCMHGSC_JDW ss91150481 Mar 24, 2008 (129)
4 ENSEMBL ss138438166 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss164329219 Jul 04, 2010 (132)
6 BL ss253087557 May 09, 2011 (134)
7 GMI ss276454745 May 04, 2012 (137)
8 1000GENOMES ss329598586 May 09, 2011 (134)
9 TISHKOFF ss555538978 Apr 25, 2013 (138)
10 SSMP ss649122109 Apr 25, 2013 (138)
11 EVA-GONL ss976784336 Aug 21, 2014 (142)
12 JMKIDD_LAB ss1069080957 Aug 21, 2014 (142)
13 1000GENOMES ss1297045787 Aug 21, 2014 (142)
14 DDI ss1428565142 Apr 01, 2015 (144)
15 EVA_GENOME_DK ss1578860909 Apr 01, 2015 (144)
16 EVA_DECODE ss1586194364 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1603414915 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1646408948 Apr 01, 2015 (144)
19 WEILL_CORNELL_DGM ss1920019373 Feb 12, 2016 (147)
20 JJLAB ss2020543299 Sep 14, 2016 (149)
21 USC_VALOUEV ss2148587310 Dec 20, 2016 (150)
22 HUMAN_LONGEVITY ss2229880424 Dec 20, 2016 (150)
23 TOPMED ss2395811076 Dec 20, 2016 (150)
24 SYSTEMSBIOZJU ss2624783786 Nov 08, 2017 (151)
25 GRF ss2703153449 Nov 08, 2017 (151)
26 GNOMAD ss2772923622 Nov 08, 2017 (151)
27 SWEGEN ss2989430731 Nov 08, 2017 (151)
28 BIOINF_KMB_FNS_UNIBA ss3024037471 Nov 08, 2017 (151)
29 TOPMED ss3306661086 Nov 08, 2017 (151)
30 CSHL ss3344208626 Nov 08, 2017 (151)
31 1000Genomes NC_000002.11 - 47481641 Oct 11, 2018 (152)
32 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 47481641 Oct 11, 2018 (152)
33 Genetic variation in the Estonian population NC_000002.11 - 47481641 Oct 11, 2018 (152)
34 gnomAD - Genomes NC_000002.11 - 47481641 Oct 11, 2018 (152)
35 TopMed NC_000002.12 - 47254502 Oct 11, 2018 (152)
36 UK 10K study - Twins NC_000002.11 - 47481641 Oct 11, 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
ss78385671 NC_000002.9:47393291:A= NC_000002.12:47254501:A= (self)
ss91150481, ss164329219, ss253087557, ss276454745, ss1586194364 NC_000002.10:47335144:A= NC_000002.12:47254501:A= (self)
7984493, 4437226, 3134914, 102413483, 4437226, ss329598586, ss555538978, ss649122109, ss976784336, ss1069080957, ss1297045787, ss1428565142, ss1578860909, ss1603414915, ss1646408948, ss1920019373, ss2020543299, ss2148587310, ss2395811076, ss2624783786, ss2703153449, ss2772923622, ss2989430731, ss3344208626 NC_000002.11:47481640:A= NC_000002.12:47254501:A= (self)
192029417, ss2229880424, ss3024037471, ss3306661086 NC_000002.12:47254501:A= NC_000002.12:47254501:A= (self)
ss14054205 NT_022184.13:26297572:A= NC_000002.12:47254501:A= (self)
ss138438166 NT_022184.15:26303527:A= NC_000002.12:47254501:A= (self)
ss78385671 NC_000002.9:47393291:A>G NC_000002.12:47254501:A>G (self)
ss91150481, ss164329219, ss253087557, ss276454745, ss1586194364 NC_000002.10:47335144:A>G NC_000002.12:47254501:A>G (self)
7984493, 4437226, 3134914, 102413483, 4437226, ss329598586, ss555538978, ss649122109, ss976784336, ss1069080957, ss1297045787, ss1428565142, ss1578860909, ss1603414915, ss1646408948, ss1920019373, ss2020543299, ss2148587310, ss2395811076, ss2624783786, ss2703153449, ss2772923622, ss2989430731, ss3344208626 NC_000002.11:47481640:A>G NC_000002.12:47254501:A>G (self)
192029417, ss2229880424, ss3024037471, ss3306661086 NC_000002.12:47254501:A>G NC_000002.12:47254501:A>G (self)
ss14054205 NT_022184.13:26297572:A>G NC_000002.12:47254501:A>G (self)
ss138438166 NT_022184.15:26303527:A>G NC_000002.12:47254501:A>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 rs10190105

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.post58+e54ea20