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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.

rs374780253

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:297477-297482 (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
delTAA
Variation Type
Indel Insertion and Deletion
Frequency
delTAA=0.029720 (3264/109824, GnomAD)
delTAA=0.01956 (317/16204, ALFA)
delTAA=0.15601 (2473/15852, 8.3KJPN) (+ 1 more)
delTAA=0.0399 (200/5008, 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.297477TAA[1]
GRCh37.p13 chr 1 NC_000001.10:g.267228TAA[1]
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 16204 TAATAA=0.98044 TAA=0.01956
European Sub 11952 TAATAA=0.99130 TAA=0.00870
African Sub 2816 TAATAA=0.9411 TAA=0.0589
African Others Sub 108 TAATAA=0.944 TAA=0.056
African American Sub 2708 TAATAA=0.9409 TAA=0.0591
Asian Sub 108 TAATAA=0.944 TAA=0.056
East Asian Sub 84 TAATAA=0.93 TAA=0.07
Other Asian Sub 24 TAATAA=1.00 TAA=0.00
Latin American 1 Sub 146 TAATAA=0.986 TAA=0.014
Latin American 2 Sub 610 TAATAA=0.989 TAA=0.011
South Asian Sub 94 TAATAA=0.81 TAA=0.19
Other Sub 478 TAATAA=0.971 TAA=0.029


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
gnomAD - Genomes Global Study-wide 109824 (TAA)2=0.970280 delTAA=0.029720
gnomAD - Genomes European Sub 60176 (TAA)2=0.98963 delTAA=0.01037
gnomAD - Genomes African Sub 33348 (TAA)2=0.93817 delTAA=0.06183
gnomAD - Genomes American Sub 9560 (TAA)2=0.9714 delTAA=0.0286
gnomAD - Genomes Ashkenazi Jewish Sub 2858 (TAA)2=0.9895 delTAA=0.0105
gnomAD - Genomes East Asian Sub 2350 (TAA)2=0.9064 delTAA=0.0936
gnomAD - Genomes Other Sub 1532 (TAA)2=0.9641 delTAA=0.0359
Allele Frequency Aggregator Total Global 16204 (TAA)2=0.98044 delTAA=0.01956
Allele Frequency Aggregator European Sub 11952 (TAA)2=0.99130 delTAA=0.00870
Allele Frequency Aggregator African Sub 2816 (TAA)2=0.9411 delTAA=0.0589
Allele Frequency Aggregator Latin American 2 Sub 610 (TAA)2=0.989 delTAA=0.011
Allele Frequency Aggregator Other Sub 478 (TAA)2=0.971 delTAA=0.029
Allele Frequency Aggregator Latin American 1 Sub 146 (TAA)2=0.986 delTAA=0.014
Allele Frequency Aggregator Asian Sub 108 (TAA)2=0.944 delTAA=0.056
Allele Frequency Aggregator South Asian Sub 94 (TAA)2=0.81 delTAA=0.19
8.3KJPN JAPANESE Study-wide 15852 (TAA)2=0.84399 delTAA=0.15601
1000Genomes Global Study-wide 5008 (TAA)2=0.9601 delTAA=0.0399
1000Genomes African Sub 1322 (TAA)2=0.9455 delTAA=0.0545
1000Genomes East Asian Sub 1008 (TAA)2=0.9593 delTAA=0.0407
1000Genomes Europe Sub 1006 (TAA)2=0.9901 delTAA=0.0099
1000Genomes South Asian Sub 978 (TAA)2=0.929 delTAA=0.071
1000Genomes American Sub 694 (TAA)2=0.988 delTAA=0.012
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 (TAA)2= delTAA
GRCh38.p13 chr 1 NC_000001.11:g.297477_297482= NC_000001.11:g.297477TAA[1]
GRCh37.p13 chr 1 NC_000001.10:g.267228_267233= NC_000001.10:g.267228TAA[1]
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#.

10 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSMP ss663178628 Apr 01, 2015 (144)
2 SSIP ss947011658 Aug 21, 2014 (142)
3 1000GENOMES ss1367645255 Aug 21, 2014 (142)
4 EVA_DECODE ss1584129277 Apr 01, 2015 (144)
5 GNOMAD ss2750617261 Nov 08, 2017 (151)
6 SWEGEN ss2986144636 Nov 08, 2017 (151)
7 TOPMED ss3066353402 Nov 08, 2017 (151)
8 EVA_DECODE ss3685991112 Jul 12, 2019 (153)
9 KHV_HUMAN_GENOMES ss3798742700 Jul 12, 2019 (153)
10 TOMMO_GENOMICS ss5142040995 Apr 25, 2021 (155)
11 1000Genomes NC_000001.10 - 267228 Oct 11, 2018 (152)
12 gnomAD - Genomes NC_000001.11 - 297477 Apr 25, 2021 (155)
13 8.3KJPN NC_000001.10 - 267228 Apr 25, 2021 (155)
14 ALFA NC_000001.11 - 297477 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
ss1584129277 NC_000001.9:257090:TAA: NC_000001.11:297476:TAATAA:TAA (self)
1225, 10302, ss663178628, ss947011658, ss1367645255, ss2750617261, ss2986144636, ss5142040995 NC_000001.10:267227:TAA: NC_000001.11:297476:TAATAA:TAA (self)
29759, ss3066353402, ss3685991112, ss3798742700 NC_000001.11:297476:TAA: NC_000001.11:297476:TAATAA:TAA (self)
1950817594 NC_000001.11:297476:TAATAA:TAA NC_000001.11:297476:TAATAA:TAA
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 rs374780253

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