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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.

rs77573425

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:61989 (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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.13645 (2262/16578, 8.3KJPN)
C=0.3512 (2412/6868, ALFA)
C=0.1256 (363/2890, KOREAN) (+ 7 more)
C=0.1363 (247/1812, Korea1K)
C=0.443 (442/998, GoNL)
G=0.483 (277/574, NorthernSweden)
G=0.398 (117/294, SGDP_PRJ)
C=0.471 (97/206, Qatari)
G=0.35 (14/40, Siberian)
G=0.47 (18/38, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome

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 6868 G=0.6488 A=0.0000, C=0.3512
European Sub 5376 G=0.5519 A=0.0000, C=0.4481
African Sub 1020 G=1.0000 A=0.0000, C=0.0000
African Others Sub 26 G=1.00 A=0.00, C=0.00
African American Sub 994 G=1.000 A=0.000, C=0.000
Asian Sub 72 G=1.00 A=0.00, C=0.00
East Asian Sub 56 G=1.00 A=0.00, C=0.00
Other Asian Sub 16 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 40 G=1.00 A=0.00, C=0.00
Latin American 2 Sub 194 G=1.000 A=0.000, C=0.000
South Asian Sub 28 G=1.00 A=0.00, C=0.00
Other Sub 138 G=0.978 A=0.000, C=0.022


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
8.3KJPN JAPANESE Study-wide 16578 G=0.86355 C=0.13645
KOREAN population from KRGDB KOREAN Study-wide 2890 G=0.8744 C=0.1256
Korean Genome Project KOREAN Study-wide 1812 G=0.8637 C=0.1363
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.557 C=0.443
Northern Sweden ACPOP Study-wide 574 G=0.483 C=0.517
SGDP_PRJ Global Study-wide 294 G=0.398 C=0.602
Qatari Global Study-wide 206 G=0.529 C=0.471
Siberian Global Study-wide 40 G=0.35 C=0.65
The Danish reference pan genome Danish Study-wide 38 G=0.47 C=0.53
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.61989G>A
GRCh38.p13 chr 1 NC_000001.11:g.61989G>C
GRCh37.p13 chr 1 NC_000001.10:g.61989G>A
GRCh37.p13 chr 1 NC_000001.10:g.61989G>C
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

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 C
GRCh38.p13 chr 1 NC_000001.11:g.61989= NC_000001.11:g.61989G>A NC_000001.11:g.61989G>C
GRCh37.p13 chr 1 NC_000001.10:g.61989= NC_000001.10:g.61989G>A NC_000001.10:g.61989G>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#.

25 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 ENSEMBL ss137751563 Dec 01, 2009 (131)
2 BL ss252863953 May 09, 2011 (134)
3 1000GENOMES ss328356537 May 09, 2011 (134)
4 EVA-GONL ss974768763 Aug 21, 2014 (142)
5 JMKIDD_LAB ss1067612303 Aug 21, 2014 (142)
6 DDI ss1425684556 Apr 01, 2015 (144)
7 EVA_GENOME_DK ss1573850722 Apr 01, 2015 (144)
8 WEILL_CORNELL_DGM ss1917958266 Feb 12, 2016 (147)
9 JJLAB ss2019497541 Sep 14, 2016 (149)
10 BIOINF_KMB_FNS_UNIBA ss2137543876 Oct 11, 2018 (152)
11 USC_VALOUEV ss2147483704 Dec 20, 2016 (150)
12 GRF ss2697373009 Nov 08, 2017 (151)
13 GNOMAD ss2750604269 Nov 08, 2017 (151)
14 SWEGEN ss2986142015 Nov 08, 2017 (151)
15 TOPMED ss3066322052 Nov 08, 2017 (151)
16 TOPMED ss3066322053 Nov 08, 2017 (151)
17 CSHL ss3343271556 Nov 08, 2017 (151)
18 URBANLAB ss3646580392 Oct 11, 2018 (152)
19 ACPOP ss3726715203 Jul 12, 2019 (153)
20 EVA ss3745720534 Jul 12, 2019 (153)
21 EVA ss3825981331 Apr 25, 2020 (154)
22 SGDP_PRJ ss3847984069 Apr 25, 2020 (154)
23 KRGDB ss3892823909 Apr 25, 2020 (154)
24 KOGIC ss3943622660 Apr 25, 2020 (154)
25 TOMMO_GENOMICS ss5142032923 Apr 25, 2021 (155)
26 The Danish reference pan genome NC_000001.10 - 61989 Apr 25, 2020 (154)
27 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 5081 (NC_000001.11:61988:G:A 5/127606)
Row 5082 (NC_000001.11:61988:G:C 54289/118470)

- Apr 25, 2021 (155)
28 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 5081 (NC_000001.11:61988:G:A 5/127606)
Row 5082 (NC_000001.11:61988:G:C 54289/118470)

- Apr 25, 2021 (155)
29 Genome of the Netherlands Release 5 NC_000001.10 - 61989 Apr 25, 2020 (154)
30 KOREAN population from KRGDB NC_000001.10 - 61989 Apr 25, 2020 (154)
31 Korean Genome Project NC_000001.11 - 61989 Apr 25, 2020 (154)
32 Northern Sweden NC_000001.10 - 61989 Jul 12, 2019 (153)
33 Qatari NC_000001.10 - 61989 Apr 25, 2020 (154)
34 SGDP_PRJ NC_000001.10 - 61989 Apr 25, 2020 (154)
35 Siberian NC_000001.10 - 61989 Apr 25, 2020 (154)
36 8.3KJPN NC_000001.10 - 61989 Apr 25, 2021 (155)
37 ALFA NC_000001.11 - 61989 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
10281576713, ss3066322052 NC_000001.11:61988:G:A NC_000001.11:61988:G:A (self)
ss252863953 NC_000001.9:51851:G:C NC_000001.11:61988:G:C (self)
1357956, 19, 1303, 68, 196, 1049, 58, 2230, ss328356537, ss974768763, ss1067612303, ss1425684556, ss1573850722, ss1917958266, ss2019497541, ss2147483704, ss2697373009, ss2750604269, ss2986142015, ss3343271556, ss3726715203, ss3745720534, ss3825981331, ss3847984069, ss3892823909, ss5142032923 NC_000001.10:61988:G:C NC_000001.11:61988:G:C (self)
661, 10281576713, ss2137543876, ss3066322053, ss3646580392, ss3943622660 NC_000001.11:61988:G:C NC_000001.11:61988:G:C (self)
ss137751563 NT_077402.2:51988:G:C NC_000001.11:61988:G:C (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 rs77573425

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.post629+eb05767