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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.

rs147402771

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1125950-1125956 (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
delA / dupA
Variation Type
Indel Insertion and Deletion
Frequency
delA=0.00000 (0/13974, ALFA)
dupA=0.00000 (0/13974, ALFA)
dupA=0.0036 (18/5008, 1000G)
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.1125956del
GRCh38.p13 chr 1 NC_000001.11:g.1125956dup
GRCh37.p13 chr 1 NC_000001.10:g.1061336del
GRCh37.p13 chr 1 NC_000001.10:g.1061336dup
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 13974 AAAAAAA=1.00000 AAAAAA=0.00000, AAAAAAAA=0.00000
European Sub 9686 AAAAAAA=1.0000 AAAAAA=0.0000, AAAAAAAA=0.0000
African Sub 2832 AAAAAAA=1.0000 AAAAAA=0.0000, AAAAAAAA=0.0000
African Others Sub 112 AAAAAAA=1.000 AAAAAA=0.000, AAAAAAAA=0.000
African American Sub 2720 AAAAAAA=1.0000 AAAAAA=0.0000, AAAAAAAA=0.0000
Asian Sub 112 AAAAAAA=1.000 AAAAAA=0.000, AAAAAAAA=0.000
East Asian Sub 86 AAAAAAA=1.00 AAAAAA=0.00, AAAAAAAA=0.00
Other Asian Sub 26 AAAAAAA=1.00 AAAAAA=0.00, AAAAAAAA=0.00
Latin American 1 Sub 146 AAAAAAA=1.000 AAAAAA=0.000, AAAAAAAA=0.000
Latin American 2 Sub 608 AAAAAAA=1.000 AAAAAA=0.000, AAAAAAAA=0.000
South Asian Sub 98 AAAAAAA=1.00 AAAAAA=0.00, AAAAAAAA=0.00
Other Sub 492 AAAAAAA=1.000 AAAAAA=0.000, AAAAAAAA=0.000


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
1000Genomes Global Study-wide 5008 -

No frequency provided

dupA=0.0036
1000Genomes African Sub 1322 -

No frequency provided

dupA=0.0136
1000Genomes East Asian Sub 1008 -

No frequency provided

dupA=0.0000
1000Genomes Europe Sub 1006 -

No frequency provided

dupA=0.0000
1000Genomes South Asian Sub 978 -

No frequency provided

dupA=0.000
1000Genomes American Sub 694 -

No frequency provided

dupA=0.000
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)7= delA dupA
GRCh38.p13 chr 1 NC_000001.11:g.1125950_1125956= NC_000001.11:g.1125956del NC_000001.11:g.1125956dup
GRCh37.p13 chr 1 NC_000001.10:g.1061330_1061336= NC_000001.10:g.1061336del NC_000001.10:g.1061336dup
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#.

12 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss325997353 May 09, 2011 (134)
2 LUNTER ss550899295 Apr 25, 2013 (138)
3 TISHKOFF ss553747754 Apr 25, 2013 (138)
4 1000GENOMES ss1367645860 Aug 21, 2014 (142)
5 TOPMED ss2321526180 Dec 20, 2016 (150)
6 GNOMAD ss2750672781 Nov 08, 2017 (151)
7 TOPMED ss3066474337 Nov 08, 2017 (151)
8 TOPMED ss3066474338 Nov 08, 2017 (151)
9 EVA_DECODE ss3685998148 Jul 12, 2019 (153)
10 GNOMAD ss3986971141 Apr 25, 2021 (155)
11 TOPMED ss4436522706 Apr 25, 2021 (155)
12 TOPMED ss4436522707 Apr 25, 2021 (155)
13 1000Genomes NC_000001.10 - 1061330 Oct 11, 2018 (152)
14 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 144137 (NC_000001.11:1125949::A 413/140214)
Row 144138 (NC_000001.11:1125949:A: 1/140216)

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

Submission ignored due to conflicting rows:
Row 144137 (NC_000001.11:1125949::A 413/140214)
Row 144138 (NC_000001.11:1125949:A: 1/140216)

- Apr 25, 2021 (155)
16 TopMed

Submission ignored due to conflicting rows:
Row 73083 (NC_000001.11:1125949::A 380/125568)
Row 73084 (NC_000001.11:1125949:A: 3/125568)

- Oct 11, 2018 (152)
17 TopMed

Submission ignored due to conflicting rows:
Row 129041 (NC_000001.11:1125949::A 782/264690)
Row 129042 (NC_000001.11:1125949:A: 4/264690)

- Apr 25, 2021 (155)
18 TopMed

Submission ignored due to conflicting rows:
Row 129041 (NC_000001.11:1125949::A 782/264690)
Row 129042 (NC_000001.11:1125949:A: 4/264690)

- Apr 25, 2021 (155)
19 ALFA NC_000001.11 - 1125950 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)
rs369983039 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3066474338, ss3986971141, ss4436522707 NC_000001.11:1125949:A: NC_000001.11:1125949:AAAAAAA:AAAAAA (self)
12767410847 NC_000001.11:1125949:AAAAAAA:AAAAAA NC_000001.11:1125949:AAAAAAA:AAAAAA (self)
ss325997353, ss550899295 NC_000001.9:1051192::A NC_000001.11:1125949:AAAAAAA:AAAAA…

NC_000001.11:1125949:AAAAAAA:AAAAAAAA

(self)
15776, ss1367645860, ss2321526180, ss2750672781 NC_000001.10:1061329::A NC_000001.11:1125949:AAAAAAA:AAAAA…

NC_000001.11:1125949:AAAAAAA:AAAAAAAA

(self)
ss553747754 NC_000001.10:1061336::A NC_000001.11:1125949:AAAAAAA:AAAAA…

NC_000001.11:1125949:AAAAAAA:AAAAAAAA

(self)
ss3066474337, ss3685998148, ss4436522706 NC_000001.11:1125949::A NC_000001.11:1125949:AAAAAAA:AAAAA…

NC_000001.11:1125949:AAAAAAA:AAAAAAAA

(self)
12767410847 NC_000001.11:1125949:AAAAAAA:AAAAA…

NC_000001.11:1125949:AAAAAAA:AAAAAAAA

NC_000001.11:1125949:AAAAAAA:AAAAA…

NC_000001.11:1125949:AAAAAAA:AAAAAAAA

(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 rs147402771

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