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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.

rs149555176

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1123500-1123512 (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
delCT(GCAC)2
Variation Type
Indel Insertion and Deletion
Frequency
delCT(GCAC)2=0.002958 (783/264690, TOPMED)
delCT(GCAC)2=0.002955 (413/139758, GnomAD)
delCT(GCAC)2=0.00263 (37/14050, ALFA) (+ 2 more)
delCT(GCAC)2=0.0000 (0/3854, ALSPAC)
delCT(GCAC)2=0.0003 (1/3708, 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.1123503_1123512del
GRCh37.p13 chr 1 NC_000001.10:g.1058883_1058892del
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 14050 CACCTGCACGCAC=0.99737 CAC=0.00263
European Sub 9690 CACCTGCACGCAC=1.0000 CAC=0.0000
African Sub 2898 CACCTGCACGCAC=0.9883 CAC=0.0117
African Others Sub 114 CACCTGCACGCAC=0.991 CAC=0.009
African American Sub 2784 CACCTGCACGCAC=0.9881 CAC=0.0119
Asian Sub 112 CACCTGCACGCAC=1.000 CAC=0.000
East Asian Sub 86 CACCTGCACGCAC=1.00 CAC=0.00
Other Asian Sub 26 CACCTGCACGCAC=1.00 CAC=0.00
Latin American 1 Sub 146 CACCTGCACGCAC=1.000 CAC=0.000
Latin American 2 Sub 610 CACCTGCACGCAC=0.998 CAC=0.002
South Asian Sub 98 CACCTGCACGCAC=1.00 CAC=0.00
Other Sub 496 CACCTGCACGCAC=0.996 CAC=0.004


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
TopMed Global Study-wide 264690 CACCT(GCAC)2=0.997042 delCT(GCAC)2=0.002958
gnomAD - Genomes Global Study-wide 139758 CACCT(GCAC)2=0.997045 delCT(GCAC)2=0.002955
gnomAD - Genomes European Sub 75844 CACCT(GCAC)2=0.99996 delCT(GCAC)2=0.00004
gnomAD - Genomes African Sub 41674 CACCT(GCAC)2=0.99047 delCT(GCAC)2=0.00953
gnomAD - Genomes American Sub 13642 CACCT(GCAC)2=0.99941 delCT(GCAC)2=0.00059
gnomAD - Genomes Ashkenazi Jewish Sub 3320 CACCT(GCAC)2=1.0000 delCT(GCAC)2=0.0000
gnomAD - Genomes East Asian Sub 3130 CACCT(GCAC)2=1.0000 delCT(GCAC)2=0.0000
gnomAD - Genomes Other Sub 2148 CACCT(GCAC)2=0.9977 delCT(GCAC)2=0.0023
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 CACCT(GCAC)2=1.0000 delCT(GCAC)2=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 CACCT(GCAC)2=0.9997 delCT(GCAC)2=0.0003
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 CACCT(GCAC)2= delCT(GCAC)2
GRCh38.p13 chr 1 NC_000001.11:g.1123500_1123512= NC_000001.11:g.1123503_1123512del
GRCh37.p13 chr 1 NC_000001.10:g.1058880_1058892= NC_000001.10:g.1058883_1058892del
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#.

9 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss325997349 May 09, 2011 (134)
2 LUNTER ss550899292 Apr 25, 2013 (138)
3 TISHKOFF ss553708601 Apr 25, 2013 (138)
4 EVA_UK10K_ALSPAC ss1700146449 Apr 01, 2015 (144)
5 EVA_UK10K_TWINSUK ss1700155009 Apr 01, 2015 (144)
6 TOPMED ss2321525964 Dec 20, 2016 (150)
7 TOPMED ss3066473552 Nov 08, 2017 (151)
8 GNOMAD ss3986970575 Apr 25, 2021 (155)
9 TOPMED ss4436521873 Apr 25, 2021 (155)
10 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1058880 Oct 11, 2018 (152)
11 gnomAD - Genomes NC_000001.11 - 1123500 Apr 25, 2021 (155)
12 TopMed NC_000001.11 - 1123500 Apr 25, 2021 (155)
13 UK 10K study - Twins NC_000001.10 - 1058880 Oct 11, 2018 (152)
14 ALFA NC_000001.11 - 1123500 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
ss325997349, ss550899292 NC_000001.9:1048742:CACCTGCACG: NC_000001.11:1123499:CACCTGCACGCAC…

NC_000001.11:1123499:CACCTGCACGCAC:CAC

(self)
5066, 5066, ss1700146449, ss1700155009, ss2321525964 NC_000001.10:1058879:CACCTGCACG: NC_000001.11:1123499:CACCTGCACGCAC…

NC_000001.11:1123499:CACCTGCACGCAC:CAC

(self)
ss553708601 NC_000001.10:1058882:CTGCACGCAC: NC_000001.11:1123499:CACCTGCACGCAC…

NC_000001.11:1123499:CACCTGCACGCAC:CAC

(self)
143212, 72575, 128208, ss3066473552, ss3986970575, ss4436521873 NC_000001.11:1123499:CACCTGCACG: NC_000001.11:1123499:CACCTGCACGCAC…

NC_000001.11:1123499:CACCTGCACGCAC:CAC

(self)
3006719795 NC_000001.11:1123499:CACCTGCACGCAC…

NC_000001.11:1123499:CACCTGCACGCAC:CAC

NC_000001.11:1123499:CACCTGCACGCAC…

NC_000001.11:1123499:CACCTGCACGCAC:CAC

(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 rs149555176

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