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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.

rs548914330

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:285678-285679 (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
dupT
Variation Type
Indel Insertion and Deletion
Frequency
dupT=0.02305 (373/16182, ALFA)
dupT=0.03771 (592/15698, 8.3KJPN)
dupT=0.0010 (5/5008, 1000G) (+ 2 more)
dupT=0.0054 (21/3854, ALSPAC)
dupT=0.0070 (26/3708, TWINSUK)
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.285679dup
GRCh37.p13 chr 1 NC_000001.10:g.255430dup
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 16182 TT=0.97695 TTT=0.02305
European Sub 11930 TT=0.97267 TTT=0.02733
African Sub 2816 TT=0.9918 TTT=0.0082
African Others Sub 108 TT=1.000 TTT=0.000
African American Sub 2708 TT=0.9915 TTT=0.0085
Asian Sub 108 TT=0.963 TTT=0.037
East Asian Sub 84 TT=0.95 TTT=0.05
Other Asian Sub 24 TT=1.00 TTT=0.00
Latin American 1 Sub 146 TT=0.979 TTT=0.021
Latin American 2 Sub 610 TT=0.984 TTT=0.016
South Asian Sub 94 TT=0.99 TTT=0.01
Other Sub 478 TT=0.987 TTT=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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
8.3KJPN JAPANESE Study-wide 15698 -

No frequency provided

dupT=0.03771
1000Genomes Global Study-wide 5008 -

No frequency provided

dupT=0.0010
1000Genomes African Sub 1322 -

No frequency provided

dupT=0.0000
1000Genomes East Asian Sub 1008 -

No frequency provided

dupT=0.0000
1000Genomes Europe Sub 1006 -

No frequency provided

dupT=0.0050
1000Genomes South Asian Sub 978 -

No frequency provided

dupT=0.000
1000Genomes American Sub 694 -

No frequency provided

dupT=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 -

No frequency provided

dupT=0.0054
UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

dupT=0.0070
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 TT= dupT
GRCh38.p13 chr 1 NC_000001.11:g.285678_285679= NC_000001.11:g.285679dup
GRCh37.p13 chr 1 NC_000001.10:g.255429_255430= NC_000001.10:g.255430dup
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#.

8 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1367645250 Aug 21, 2014 (142)
2 EVA_DECODE ss1584129276 Apr 01, 2015 (144)
3 EVA_UK10K_ALSPAC ss1700140435 Apr 01, 2015 (144)
4 EVA_UK10K_TWINSUK ss1700153113 Apr 01, 2015 (144)
5 GNOMAD ss2750616662 Nov 08, 2017 (151)
6 SWEGEN ss2986144531 Nov 08, 2017 (151)
7 TOPMED ss3066351859 Nov 08, 2017 (151)
8 TOMMO_GENOMICS ss5142040666 Apr 25, 2021 (155)
9 1000Genomes NC_000001.10 - 255429 Oct 11, 2018 (152)
10 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 255429 Oct 11, 2018 (152)
11 8.3KJPN NC_000001.10 - 255429 Apr 25, 2021 (155)
12 UK 10K study - Twins NC_000001.10 - 255429 Oct 11, 2018 (152)
13 ALFA NC_000001.11 - 285678 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
ss1584129276 NC_000001.9:245291::T NC_000001.11:285677:TT:TTT (self)
1196, 36, 9973, 36, ss1367645250, ss1700140435, ss1700153113, ss2750616662, ss2986144531, ss5142040666 NC_000001.10:255428::T NC_000001.11:285677:TT:TTT (self)
ss3066351859 NC_000001.11:285677::T NC_000001.11:285677:TT:TTT (self)
2984054959 NC_000001.11:285677:TT:TTT NC_000001.11:285677:TT:TTT
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 rs548914330

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