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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.

rs3844233

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:62777 (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
A>C / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.12076 (2002/16578, 8.3KJPN)
T=0.3154 (2305/7308, ALFA)
T=0.2564 (1284/5008, 1000G) (+ 4 more)
T=0.1117 (321/2874, KOREAN)
T=0.1257 (228/1814, Korea1K)
A=0.493 (284/576, NorthernSweden)
A=0.375 (87/232, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.62777A>C
GRCh38.p13 chr 1 NC_000001.11:g.62777A>T
GRCh37.p13 chr 1 NC_000001.10:g.62777A>C
GRCh37.p13 chr 1 NC_000001.10:g.62777A>T
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 7308 A=0.6846 C=0.0000, T=0.3154
European Sub 5570 A=0.5865 C=0.0000, T=0.4135
African Sub 1208 A=1.0000 C=0.0000, T=0.0000
African Others Sub 34 A=1.00 C=0.00, T=0.00
African American Sub 1174 A=1.0000 C=0.0000, T=0.0000
Asian Sub 74 A=1.00 C=0.00, T=0.00
East Asian Sub 58 A=1.00 C=0.00, T=0.00
Other Asian Sub 16 A=1.00 C=0.00, T=0.00
Latin American 1 Sub 48 A=1.00 C=0.00, T=0.00
Latin American 2 Sub 220 A=1.000 C=0.000, T=0.000
South Asian Sub 38 A=1.00 C=0.00, T=0.00
Other Sub 150 A=0.987 C=0.000, T=0.013


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
8.3KJPN JAPANESE Study-wide 16578 A=0.87924 T=0.12076
Allele Frequency Aggregator Total Global 7308 A=0.6846 C=0.0000, T=0.3154
Allele Frequency Aggregator European Sub 5570 A=0.5865 C=0.0000, T=0.4135
Allele Frequency Aggregator African Sub 1208 A=1.0000 C=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 220 A=1.000 C=0.000, T=0.000
Allele Frequency Aggregator Other Sub 150 A=0.987 C=0.000, T=0.013
Allele Frequency Aggregator Asian Sub 74 A=1.00 C=0.00, T=0.00
Allele Frequency Aggregator Latin American 1 Sub 48 A=1.00 C=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 38 A=1.00 C=0.00, T=0.00
1000Genomes Global Study-wide 5008 A=0.7436 T=0.2564
1000Genomes African Sub 1322 A=0.8200 T=0.1800
1000Genomes East Asian Sub 1008 A=0.9325 T=0.0675
1000Genomes Europe Sub 1006 A=0.5467 T=0.4533
1000Genomes South Asian Sub 978 A=0.681 T=0.319
1000Genomes American Sub 694 A=0.697 T=0.303
KOREAN population from KRGDB KOREAN Study-wide 2874 A=0.8883 T=0.1117
Korean Genome Project KOREAN Study-wide 1814 A=0.8743 T=0.1257
Northern Sweden ACPOP Study-wide 576 A=0.493 T=0.507
SGDP_PRJ Global Study-wide 232 A=0.375 C=0.004, T=0.621
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= C T
GRCh38.p13 chr 1 NC_000001.11:g.62777= NC_000001.11:g.62777A>C NC_000001.11:g.62777A>T
GRCh37.p13 chr 1 NC_000001.10:g.62777= NC_000001.10:g.62777A>C NC_000001.10:g.62777A>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#.

23 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss5379901 Oct 08, 2002 (108)
2 TSC-CSHL ss5380796 Oct 08, 2002 (108)
3 TSC-CSHL ss5380851 Oct 08, 2002 (108)
4 SC_JCM ss6286699 Feb 20, 2003 (113)
5 BCMHGSC_JDW ss87153258 Mar 25, 2008 (130)
6 ENSEMBL ss161695330 Dec 01, 2009 (131)
7 1000GENOMES ss1289335765 Aug 21, 2014 (144)
8 DDI ss1425684558 Apr 01, 2015 (144)
9 PADH-LAB_SPU ss1713846948 Sep 08, 2015 (146)
10 JJLAB ss2019497542 Sep 14, 2016 (149)
11 GRF ss2697373014 Nov 08, 2017 (151)
12 GNOMAD ss2750604362 Nov 08, 2017 (151)
13 SWEGEN ss2986142034 Nov 08, 2017 (151)
14 TOPMED ss3066322275 Nov 08, 2017 (151)
15 TOPMED ss3066322276 Nov 08, 2017 (151)
16 CSHL ss3343271563 Nov 08, 2017 (151)
17 URBANLAB ss3646580395 Oct 11, 2018 (152)
18 ACPOP ss3726715207 Jul 12, 2019 (153)
19 KHV_HUMAN_GENOMES ss3798742481 Jul 12, 2019 (153)
20 SGDP_PRJ ss3847984102 Apr 25, 2020 (154)
21 KRGDB ss3892823926 Apr 25, 2020 (154)
22 KOGIC ss3943622674 Apr 25, 2020 (154)
23 TOMMO_GENOMICS ss5142032970 Apr 25, 2021 (155)
24 1000Genomes NC_000001.10 - 62777 Oct 11, 2018 (152)
25 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 5261 (NC_000001.11:62776:A:C 311/115890)
Row 5262 (NC_000001.11:62776:A:T 40005/100220)

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

Submission ignored due to conflicting rows:
Row 5261 (NC_000001.11:62776:A:C 311/115890)
Row 5262 (NC_000001.11:62776:A:T 40005/100220)

- Apr 25, 2021 (155)
27 KOREAN population from KRGDB NC_000001.10 - 62777 Apr 25, 2020 (154)
28 Korean Genome Project NC_000001.11 - 62777 Apr 25, 2020 (154)
29 Northern Sweden NC_000001.10 - 62777 Jul 12, 2019 (153)
30 SGDP_PRJ NC_000001.10 - 62777 Apr 25, 2020 (154)
31 8.3KJPN NC_000001.10 - 62777 Apr 25, 2021 (155)
32 ALFA NC_000001.11 - 62777 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).

Associated ID History Updated (Build)
rs4631637 Mar 31, 2003 (113)
rs62637822 May 25, 2008 (130)
rs528401309 Jul 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
1082, ss2750604362, ss3847984102 NC_000001.10:62776:A:C NC_000001.11:62776:A:C (self)
189486101, ss3066322275 NC_000001.11:62776:A:C NC_000001.11:62776:A:C (self)
ss87153258 NC_000001.9:52639:A:T NC_000001.11:62776:A:T (self)
342, 1320, 72, 1082, 2277, ss1289335765, ss1425684558, ss1713846948, ss2019497542, ss2697373014, ss2750604362, ss2986142034, ss3343271563, ss3726715207, ss3847984102, ss3892823926, ss5142032970 NC_000001.10:62776:A:T NC_000001.11:62776:A:T (self)
675, 189486101, ss3066322276, ss3646580395, ss3798742481, ss3943622674 NC_000001.11:62776:A:T NC_000001.11:62776:A:T (self)
ss5379901, ss5380796, ss5380851, ss6286699, ss161695330 NT_077402.2:52776:A:T NC_000001.11:62776:A: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 rs3844233

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