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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1491415133

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:57375710-57375712 (GRCh38.p14) 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
delCA
Variation Type
Indel Insertion and Deletion
Frequency
delCA=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CGNL1 : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 11862 ACA=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 ACA=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 ACA=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 ACA=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 ACA=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 ACA=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 ACA=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 ACA=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 ACA=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 ACA=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 ACA=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 470 ACA=1.000 A=0.000 1.0 0.0 0.0 N/A


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
Allele Frequency Aggregator Total Global 11862 ACA=1.00000 delCA=0.00000
Allele Frequency Aggregator European Sub 7618 ACA=1.0000 delCA=0.0000
Allele Frequency Aggregator African Sub 2816 ACA=1.0000 delCA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 ACA=1.000 delCA=0.000
Allele Frequency Aggregator Other Sub 470 ACA=1.000 delCA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 ACA=1.000 delCA=0.000
Allele Frequency Aggregator Asian Sub 108 ACA=1.000 delCA=0.000
Allele Frequency Aggregator South Asian Sub 94 ACA=1.00 delCA=0.00
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.p14 chr 15 NC_000015.10:g.57375711_57375712del
GRCh37.p13 chr 15 NC_000015.9:g.57667909_57667910del
CGNL1 RefSeqGene NG_030584.2:g.4207_4208del
Gene: CGNL1, cingulin like 1 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
CGNL1 transcript variant 1 NM_001252335.2:c. N/A Upstream Transcript Variant
CGNL1 transcript variant 2 NM_032866.5:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X2 XM_005254726.5:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X1 XM_011522120.2:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X14 XM_011522121.3:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X4 XM_047433178.1:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X6 XM_047433180.1:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X8 XM_047433182.1:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X10 XM_047433184.1:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X11 XM_047433185.1:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X12 XM_047433186.1:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X13 XM_047433187.1:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X15 XM_047433188.1:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X17 XM_047433190.1:c. N/A Upstream Transcript Variant
CGNL1 transcript variant X3 XM_005254727.6:c. N/A N/A
CGNL1 transcript variant X18 XM_017022686.2:c. N/A N/A
CGNL1 transcript variant X5 XM_047433179.1:c. N/A N/A
CGNL1 transcript variant X7 XM_047433181.1:c. N/A N/A
CGNL1 transcript variant X9 XM_047433183.1:c. N/A N/A
CGNL1 transcript variant X16 XM_047433189.1:c. N/A N/A
CGNL1 transcript variant X19 XM_047433191.1:c. N/A N/A
CGNL1 transcript variant X20 XM_047433192.1:c. N/A N/A
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
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 ACA= delCA
GRCh38.p14 chr 15 NC_000015.10:g.57375710_57375712= NC_000015.10:g.57375711_57375712del
GRCh37.p13 chr 15 NC_000015.9:g.57667908_57667910= NC_000015.9:g.57667909_57667910del
CGNL1 RefSeqGene NG_030584.2:g.4206_4208= NG_030584.2:g.4207_4208del
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#.

1 Frequency submission
No Submitter Submission ID Date (Build)
1 ALFA NC_000015.10 - 57375710 Apr 26, 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
197549274 NC_000015.10:57375709:ACA:A NC_000015.10:57375709:ACA:A (self)
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
ss3228707678 NC_000015.10:57375709:AC: NC_000015.10:57375709:ACA:A
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 rs1491415133

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.post820+afb47a3d