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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 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.

rs72631875

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:770502 (GRCh38.p13) 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=0.052235 (13826/264690, TOPMED)
A=0.054536 (7263/133178, GnomAD)
A=0.05458 (1031/18890, ALFA) (+ 9 more)
A=0.0315 (158/5008, 1000G)
A=0.083 (83/998, GoNL)
A=0.072 (43/600, NorthernSweden)
A=0.091 (19/208, Qatari)
A=0.03 (1/40, GENOME_DK)
G=0.50 (10/20, SGDP_PRJ)
A=0.50 (10/20, SGDP_PRJ)
G=0.5 (5/10, Siberian)
A=0.5 (5/10, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC100288069 : 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.p13 chr 1 NC_000001.11:g.770502G>A
GRCh37.p13 chr 1 NC_000001.10:g.705882G>A
Gene: LOC100288069, uncharacterized LOC100288069 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC100288069 transcript NR_168328.1: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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 G=0.94542 A=0.05458
European Sub 14286 G=0.93448 A=0.06552
African Sub 2946 G=0.9895 A=0.0105
African Others Sub 114 G=1.000 A=0.000
African American Sub 2832 G=0.9891 A=0.0109
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.918 A=0.082
Latin American 2 Sub 610 G=0.959 A=0.041
South Asian Sub 98 G=0.96 A=0.04
Other Sub 692 G=0.967 A=0.033


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 G=0.947765 A=0.052235
gnomAD - Genomes Global Study-wide 133178 G=0.945464 A=0.054536
gnomAD - Genomes European Sub 75792 G=0.93094 A=0.06906
gnomAD - Genomes African Sub 35468 G=0.98153 A=0.01847
gnomAD - Genomes American Sub 13402 G=0.93770 A=0.06230
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.8733 A=0.1267
gnomAD - Genomes East Asian Sub 3122 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2072 G=0.9435 A=0.0565
1000Genomes Global Study-wide 5008 G=0.9685 A=0.0315
1000Genomes African Sub 1322 G=0.9970 A=0.0030
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9225 A=0.0775
1000Genomes South Asian Sub 978 G=0.972 A=0.028
1000Genomes American Sub 694 G=0.929 A=0.071
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.917 A=0.083
Northern Sweden ACPOP Study-wide 600 G=0.928 A=0.072
Qatari Global Study-wide 208 G=0.909 A=0.091
The Danish reference pan genome Danish Study-wide 40 G=0.97 A=0.03
SGDP_PRJ Global Study-wide 20 G=0.50 A=0.50
Siberian Global Study-wide 10 G=0.5 A=0.5
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
GRCh38.p13 chr 1 NC_000001.11:g.770502= NC_000001.11:g.770502G>A
GRCh37.p13 chr 1 NC_000001.10:g.705882= NC_000001.10:g.705882G>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#.

23 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss107938259 Feb 13, 2009 (130)
2 1000GENOMES ss230395399 Jul 14, 2010 (132)
3 BL ss252863996 May 09, 2011 (134)
4 EVA-GONL ss974769019 Aug 21, 2014 (142)
5 1000GENOMES ss1289337766 Aug 21, 2014 (142)
6 DDI ss1425684718 Apr 01, 2015 (144)
7 EVA_GENOME_DK ss1573851045 Apr 01, 2015 (144)
8 EVA_DECODE ss1584129313 Apr 01, 2015 (144)
9 WEILL_CORNELL_DGM ss1917959641 Feb 12, 2016 (147)
10 JJLAB ss2019498237 Sep 14, 2016 (149)
11 USC_VALOUEV ss2147483808 Dec 20, 2016 (150)
12 GNOMAD ss2750631860 Nov 08, 2017 (151)
13 SWEGEN ss2986147477 Nov 08, 2017 (151)
14 TOPMED ss3066386313 Nov 08, 2017 (151)
15 CSHL ss3343272149 Nov 08, 2017 (151)
16 EVA_DECODE ss3685991556 Jul 12, 2019 (153)
17 ACPOP ss3726715944 Jul 12, 2019 (153)
18 EVA ss3745720673 Jul 12, 2019 (153)
19 EVA ss3825981364 Apr 25, 2020 (154)
20 EVA ss3836378308 Apr 25, 2020 (154)
21 EVA ss3841782304 Apr 25, 2020 (154)
22 SGDP_PRJ ss3847993608 Apr 25, 2020 (154)
23 TOPMED ss4436419860 Apr 25, 2021 (155)
24 1000Genomes NC_000001.10 - 705882 Oct 11, 2018 (152)
25 The Danish reference pan genome NC_000001.10 - 705882 Apr 25, 2020 (154)
26 gnomAD - Genomes NC_000001.11 - 770502 Apr 25, 2021 (155)
27 Genome of the Netherlands Release 5 NC_000001.10 - 705882 Apr 25, 2020 (154)
28 Northern Sweden NC_000001.10 - 705882 Jul 12, 2019 (153)
29 Qatari NC_000001.10 - 705882 Apr 25, 2020 (154)
30 SGDP_PRJ NC_000001.10 - 705882 Apr 25, 2020 (154)
31 Siberian NC_000001.10 - 705882 Apr 25, 2020 (154)
32 TopMed NC_000001.11 - 770502 Apr 25, 2021 (155)
33 ALFA NC_000001.11 - 770502 Apr 25, 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
ss107938259, ss252863996, ss1584129313 NC_000001.9:695744:G:A NC_000001.11:770501:G:A (self)
2422, 1358279, 144, 809, 1571, 10588, 162, ss230395399, ss974769019, ss1289337766, ss1425684718, ss1573851045, ss1917959641, ss2019498237, ss2147483808, ss2750631860, ss2986147477, ss3343272149, ss3726715944, ss3745720673, ss3825981364, ss3836378308, ss3847993608 NC_000001.10:705881:G:A NC_000001.11:770501:G:A (self)
51506, 9443, 26195, 14624672731, ss3066386313, ss3685991556, ss3841782304, ss4436419860 NC_000001.11:770501:G:A NC_000001.11:770501: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 rs72631875

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.post596+ae089ad