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dbSNP Short Genetic Variations

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 Aliases 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.

rs626076

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr9:73419134 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.28033 (35201/125568, TOPMED)
T=0.2659 (8323/31296, GnomAD)
T=0.266 (1331/5008, 1000G) (+ 5 more)
T=0.107 (478/4480, Estonian)
T=0.099 (382/3854, ALSPAC)
T=0.112 (417/3708, TWINSUK)
T=0.10 (60/600, NorthernSweden)
T=0.05 (11/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105376083 : Intron Variant
LOC105376084 : 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 9 NC_000009.12:g.73419134G>T
GRCh37.p13 chr 9 NC_000009.11:g.76034050G>T
Gene: LOC105376083, uncharacterized LOC105376083 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105376083 transcript XR_001746729.1:n. N/A Intron Variant
Gene: LOC105376084, uncharacterized LOC105376084 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105376084 transcript variant X1 XR_929939.1:n. N/A Intron Variant
LOC105376084 transcript variant X2 XR_929940.1:n. N/A Intron Variant
LOC105376084 transcript variant X3 XR_929941.1:n. N/A Intron Variant
LOC105376084 transcript variant X4 XR_929942.1: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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 G=0.71967 T=0.28033
gnomAD - Genomes Global Study-wide 31296 G=0.7341 T=0.2659
gnomAD - Genomes European Sub 18858 G=0.8885 T=0.1115
gnomAD - Genomes African Sub 8682 G=0.320 T=0.680
gnomAD - Genomes East Asian Sub 1536 G=0.977 T=0.023
gnomAD - Genomes Other Sub 1088 G=0.853 T=0.147
gnomAD - Genomes American Sub 844 G=0.91 T=0.09
gnomAD - Genomes Ashkenazi Jewish Sub 288 G=0.84 T=0.16
1000Genomes Global Study-wide 5008 G=0.734 T=0.266
1000Genomes African Sub 1322 G=0.249 T=0.751
1000Genomes East Asian Sub 1008 G=0.967 T=0.033
1000Genomes Europe Sub 1006 G=0.893 T=0.107
1000Genomes South Asian Sub 978 G=0.87 T=0.13
1000Genomes American Sub 694 G=0.90 T=0.10
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.893 T=0.107
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.901 T=0.099
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.888 T=0.112
Northern Sweden ACPOP Study-wide 600 G=0.90 T=0.10
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.95 T=0.05
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= T Note
GRCh38.p12 chr 9 NC_000009.12:g.73419134= NC_000009.12:g.73419134G>T
GRCh37.p13 chr 9 NC_000009.11:g.76034050= NC_000009.11:g.76034050G>T
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#.

49 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss798560 Aug 11, 2000 (83)
2 WI_SSAHASNP ss12010689 Jul 11, 2003 (116)
3 WI_SSAHASNP ss14363879 Dec 05, 2003 (119)
4 HGSV ss82712753 Dec 15, 2007 (130)
5 HGSV ss84799099 Dec 15, 2007 (130)
6 HGSV ss84935425 Dec 15, 2007 (130)
7 BCMHGSC_JDW ss94083251 Mar 25, 2008 (129)
8 1000GENOMES ss114540877 Jan 25, 2009 (130)
9 ILLUMINA-UK ss115736792 Feb 14, 2009 (130)
10 ENSEMBL ss144159421 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss164199576 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss165163005 Jul 04, 2010 (132)
13 BUSHMAN ss200439732 Jul 04, 2010 (132)
14 BCM-HGSC-SUB ss206728778 Jul 04, 2010 (132)
15 1000GENOMES ss224263442 Jul 14, 2010 (132)
16 1000GENOMES ss234830396 Jul 15, 2010 (132)
17 1000GENOMES ss241603256 Jul 15, 2010 (132)
18 BL ss254294430 May 09, 2011 (134)
19 PJP ss294289171 May 09, 2011 (134)
20 TISHKOFF ss561403854 Apr 25, 2013 (138)
21 SSMP ss655890648 Apr 25, 2013 (138)
22 EVA-GONL ss986600949 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1076327047 Aug 21, 2014 (142)
24 1000GENOMES ss1334037178 Aug 21, 2014 (142)
25 DDI ss1431851089 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1583112245 Apr 01, 2015 (144)
27 EVA_DECODE ss1596230679 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1622800959 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1665794992 Apr 01, 2015 (144)
30 HAMMER_LAB ss1805999166 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1929916848 Feb 12, 2016 (147)
32 JJLAB ss2025673137 Sep 14, 2016 (149)
33 USC_VALOUEV ss2153897763 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2311535914 Dec 20, 2016 (150)
35 TOPMED ss2481904773 Dec 20, 2016 (150)
36 GRF ss2709761534 Nov 08, 2017 (151)
37 GNOMAD ss2879186504 Nov 08, 2017 (151)
38 SWEGEN ss3005011446 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3026617722 Nov 08, 2017 (151)
40 CSHL ss3348689869 Nov 08, 2017 (151)
41 TOPMED ss3591351262 Nov 08, 2017 (151)
42 EGCUT_WGS ss3672549039 Jul 13, 2019 (153)
43 EVA_DECODE ss3724049749 Jul 13, 2019 (153)
44 ACPOP ss3736562358 Jul 13, 2019 (153)
45 EVA ss3769247673 Jul 13, 2019 (153)
46 PACBIO ss3786427802 Jul 13, 2019 (153)
47 PACBIO ss3791642727 Jul 13, 2019 (153)
48 PACBIO ss3796524046 Jul 13, 2019 (153)
49 KHV_HUMAN_GENOMES ss3812416760 Jul 13, 2019 (153)
50 1000Genomes NC_000009.11 - 76034050 Oct 12, 2018 (152)
51 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 76034050 Oct 12, 2018 (152)
52 Genetic variation in the Estonian population NC_000009.11 - 76034050 Oct 12, 2018 (152)
53 gnomAD - Genomes NC_000009.11 - 76034050 Jul 13, 2019 (153)
54 Northern Sweden NC_000009.11 - 76034050 Jul 13, 2019 (153)
55 TopMed NC_000009.12 - 73419134 Oct 12, 2018 (152)
56 UK 10K study - Twins NC_000009.11 - 76034050 Oct 12, 2018 (152)
57 A Vietnamese Genetic Variation Database NC_000009.11 - 76034050 Jul 13, 2019 (153)
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)
rs59041139 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82712753, ss84799099, ss84935425 NC_000009.9:73263603:G:T NC_000009.12:73419133:G:T (self)
ss94083251, ss114540877, ss115736792, ss164199576, ss165163005, ss200439732, ss206728778, ss254294430, ss294289171, ss1596230679 NC_000009.10:75223869:G:T NC_000009.12:73419133:G:T (self)
46303082, 25711201, 18287287, 126654680, 9847223, 25711201, 5713423, ss224263442, ss234830396, ss241603256, ss561403854, ss655890648, ss986600949, ss1076327047, ss1334037178, ss1431851089, ss1583112245, ss1622800959, ss1665794992, ss1805999166, ss1929916848, ss2025673137, ss2153897763, ss2481904773, ss2709761534, ss2879186504, ss3005011446, ss3348689869, ss3672549039, ss3736562358, ss3769247673, ss3786427802, ss3791642727, ss3796524046 NC_000009.11:76034049:G:T NC_000009.12:73419133:G:T (self)
412415836, ss2311535914, ss3026617722, ss3591351262, ss3724049749, ss3812416760 NC_000009.12:73419133:G:T NC_000009.12:73419133:G:T (self)
ss798560, ss144159421 NT_008470.19:5198581:G:T NC_000009.12:73419133:G:T (self)
ss12010689 NT_023935.15:5198581:G:T NC_000009.12:73419133:G:T (self)
ss14363879 NT_023935.16:5198581:G:T NC_000009.12:73419133:G: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 rs626076

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.post308+0fe9b3b