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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.

rs1483345352

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:164841982-164841983 (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
delC
Variation Type
Indel Insertion and Deletion
Frequency
delC=0.000019 (5/264690, TOPMED)
delC=0.000036 (5/139986, GnomAD)
delC=0.000015 (2/132464, GnomAD_exome) (+ 1 more)
delC=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COBLL1 : Frameshift Variant
LOC101929633 : Intron 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 14050 CC=1.00000 C=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 CC=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 CC=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 CC=1.000 C=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 CC=1.0000 C=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 CC=1.000 C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 CC=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 CC=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CC=1.000 C=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 CC=1.000 C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 CC=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Sub 496 CC=1.000 C=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
TopMed Global Study-wide 264690 CC=0.999981 delC=0.000019
gnomAD - Genomes Global Study-wide 139986 CC=0.999964 delC=0.000036
gnomAD - Genomes European Sub 75840 CC=1.00000 delC=0.00000
gnomAD - Genomes African Sub 41910 CC=0.99988 delC=0.00012
gnomAD - Genomes American Sub 13646 CC=1.00000 delC=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 CC=1.0000 delC=0.0000
gnomAD - Genomes East Asian Sub 3124 CC=1.0000 delC=0.0000
gnomAD - Genomes Other Sub 2144 CC=1.0000 delC=0.0000
gnomAD - Exomes Global Study-wide 132464 CC=0.999985 delC=0.000015
gnomAD - Exomes European Sub 56894 CC=1.00000 delC=0.00000
gnomAD - Exomes Asian Sub 32818 CC=1.00000 delC=0.00000
gnomAD - Exomes American Sub 24344 CC=1.00000 delC=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 8168 CC=1.0000 delC=0.0000
gnomAD - Exomes African Sub 6200 CC=0.9997 delC=0.0003
gnomAD - Exomes Other Sub 4040 CC=1.0000 delC=0.0000
Allele Frequency Aggregator Total Global 14050 CC=1.00000 delC=0.00000
Allele Frequency Aggregator European Sub 9690 CC=1.0000 delC=0.0000
Allele Frequency Aggregator African Sub 2898 CC=1.0000 delC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 CC=1.000 delC=0.000
Allele Frequency Aggregator Other Sub 496 CC=1.000 delC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 CC=1.000 delC=0.000
Allele Frequency Aggregator Asian Sub 112 CC=1.000 delC=0.000
Allele Frequency Aggregator South Asian Sub 98 CC=1.00 delC=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 2 NC_000002.12:g.164841983del
GRCh37.p13 chr 2 NC_000002.11:g.165698493del
Gene: COBLL1, cordon-bleu WH2 repeat protein like 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
COBLL1 transcript variant 4 NM_001278461.2:c. N/A Genic Upstream Transcript Variant
COBLL1 transcript variant 7 NM_001365672.2:c. N/A Genic Upstream Transcript Variant
COBLL1 transcript variant 8 NM_001365673.2:c. N/A Genic Upstream Transcript Variant
COBLL1 transcript variant 9 NM_001365674.2:c. N/A Genic Upstream Transcript Variant
COBLL1 transcript variant 10 NM_001365675.2:c. N/A Genic Upstream Transcript Variant
COBLL1 transcript variant 2 NM_014900.5:c. N/A Genic Upstream Transcript Variant
COBLL1 transcript variant 6 NM_001365671.1:c.63del R [CGG] > R [CG] Coding Sequence Variant
cordon-bleu protein-like 1 isoform 6 NP_001352600.1:p.Thr22fs R (Arg) > R (Arg) Frameshift Variant
COBLL1 transcript variant 3 NM_001278460.2:c.63del R [CGG] > R [CG] Coding Sequence Variant
cordon-bleu protein-like 1 isoform 3 NP_001265389.1:p.Thr22fs R (Arg) > R (Arg) Frameshift Variant
COBLL1 transcript variant 5 NM_001365670.2:c.63del R [CGG] > R [CG] Coding Sequence Variant
cordon-bleu protein-like 1 isoform 5 NP_001352599.1:p.Thr22fs R (Arg) > R (Arg) Frameshift Variant
COBLL1 transcript variant 1 NM_001278458.2:c.63del R [CGG] > R [CG] Coding Sequence Variant
cordon-bleu protein-like 1 isoform 1 NP_001265387.1:p.Thr22fs R (Arg) > R (Arg) Frameshift Variant
Gene: LOC101929633, uncharacterized LOC101929633 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC101929633 transcript NR_110574.1:n. N/A Intron Variant
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 CC= delC
GRCh38.p14 chr 2 NC_000002.12:g.164841982_164841983= NC_000002.12:g.164841983del
GRCh37.p13 chr 2 NC_000002.11:g.165698492_165698493= NC_000002.11:g.165698493del
COBLL1 transcript variant 1 NM_001278458.2:c.62_63= NM_001278458.2:c.63del
COBLL1 transcript variant 1 NM_001278458.1:c.62_63= NM_001278458.1:c.63del
COBLL1 transcript variant 3 NM_001278460.2:c.62_63= NM_001278460.2:c.63del
COBLL1 transcript variant 3 NM_001278460.1:c.62_63= NM_001278460.1:c.63del
COBLL1 transcript variant 5 NM_001365670.2:c.62_63= NM_001365670.2:c.63del
COBLL1 transcript variant 5 NM_001365670.1:c.62_63= NM_001365670.1:c.63del
COBLL1 transcript variant 6 NM_001365671.1:c.62_63= NM_001365671.1:c.63del
cordon-bleu protein-like 1 isoform 1 NP_001265387.1:p.Arg21= NP_001265387.1:p.Thr22fs
cordon-bleu protein-like 1 isoform 3 NP_001265389.1:p.Arg21= NP_001265389.1:p.Thr22fs
cordon-bleu protein-like 1 isoform 5 NP_001352599.1:p.Arg21= NP_001352599.1:p.Thr22fs
cordon-bleu protein-like 1 isoform 6 NP_001352600.1:p.Arg21= NP_001352600.1:p.Thr22fs
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#.

4 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2733073041 Nov 08, 2017 (151)
2 GNOMAD ss2746804776 Nov 08, 2017 (151)
3 GNOMAD ss2782298573 Nov 08, 2017 (151)
4 TOPMED ss4532156877 Apr 26, 2021 (155)
5 gnomAD - Genomes NC_000002.12 - 164841982 Apr 26, 2021 (155)
6 gnomAD - Exomes NC_000002.11 - 165698492 Jul 13, 2019 (153)
7 TopMed NC_000002.12 - 164841982 Apr 26, 2021 (155)
8 ALFA NC_000002.12 - 164841982 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
2131407, ss2733073041, ss2746804776, ss2782298573 NC_000002.11:165698491:C: NC_000002.12:164841981:CC:C (self)
80543659, 335979756, ss4532156877 NC_000002.12:164841981:C: NC_000002.12:164841981:CC:C (self)
5710715286 NC_000002.12:164841981:CC:C NC_000002.12:164841981:CC:C (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 rs1483345352

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