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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.

rs377407780

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:145728350-145728356 (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
delCTG
Variation Type
Indel Insertion and Deletion
Frequency
delCTG=0.000034 (9/264690, TOPMED)
delCTG=0.000008 (2/251096, GnomAD_exome)
delCTG=0.000036 (5/140170, GnomAD) (+ 2 more)
delCTG=0.000008 (1/121150, ExAC)
delCTG=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CD160 : Inframe Deletion
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 GCTGCTG=1.00000 GCTG=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 GCTGCTG=1.0000 GCTG=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 GCTGCTG=1.0000 GCTG=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 GCTGCTG=1.000 GCTG=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 GCTGCTG=1.0000 GCTG=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 GCTGCTG=1.000 GCTG=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 GCTGCTG=1.00 GCTG=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 GCTGCTG=1.00 GCTG=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 GCTGCTG=1.000 GCTG=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 GCTGCTG=1.000 GCTG=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 GCTGCTG=1.00 GCTG=0.00 1.0 0.0 0.0 N/A
Other Sub 496 GCTGCTG=1.000 GCTG=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 (GCT)2G=0.999966 delCTG=0.000034
gnomAD - Exomes Global Study-wide 251096 (GCT)2G=0.999992 delCTG=0.000008
gnomAD - Exomes European Sub 135048 (GCT)2G=1.000000 delCTG=0.000000
gnomAD - Exomes Asian Sub 49006 (GCT)2G=1.00000 delCTG=0.00000
gnomAD - Exomes American Sub 34588 (GCT)2G=1.00000 delCTG=0.00000
gnomAD - Exomes African Sub 16240 (GCT)2G=0.99988 delCTG=0.00012
gnomAD - Exomes Ashkenazi Jewish Sub 10078 (GCT)2G=1.00000 delCTG=0.00000
gnomAD - Exomes Other Sub 6136 (GCT)2G=1.0000 delCTG=0.0000
gnomAD - Genomes Global Study-wide 140170 (GCT)2G=0.999964 delCTG=0.000036
gnomAD - Genomes European Sub 75932 (GCT)2G=1.00000 delCTG=0.00000
gnomAD - Genomes African Sub 41996 (GCT)2G=0.99990 delCTG=0.00010
gnomAD - Genomes American Sub 13638 (GCT)2G=0.99993 delCTG=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 (GCT)2G=1.0000 delCTG=0.0000
gnomAD - Genomes East Asian Sub 3134 (GCT)2G=1.0000 delCTG=0.0000
gnomAD - Genomes Other Sub 2146 (GCT)2G=1.0000 delCTG=0.0000
ExAC Global Study-wide 121150 (GCT)2G=0.999992 delCTG=0.000008
ExAC Europe Sub 73200 (GCT)2G=1.00000 delCTG=0.00000
ExAC Asian Sub 25132 (GCT)2G=1.00000 delCTG=0.00000
ExAC American Sub 11560 (GCT)2G=1.00000 delCTG=0.00000
ExAC African Sub 10352 (GCT)2G=0.99990 delCTG=0.00010
ExAC Other Sub 906 (GCT)2G=1.000 delCTG=0.000
Allele Frequency Aggregator Total Global 14050 (GCT)2G=1.00000 delCTG=0.00000
Allele Frequency Aggregator European Sub 9690 (GCT)2G=1.0000 delCTG=0.0000
Allele Frequency Aggregator African Sub 2898 (GCT)2G=1.0000 delCTG=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (GCT)2G=1.000 delCTG=0.000
Allele Frequency Aggregator Other Sub 496 (GCT)2G=1.000 delCTG=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (GCT)2G=1.000 delCTG=0.000
Allele Frequency Aggregator Asian Sub 112 (GCT)2G=1.000 delCTG=0.000
Allele Frequency Aggregator South Asian Sub 98 (GCT)2G=1.00 delCTG=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 1 NC_000001.11:g.145728351CTG[1]
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.2543764CTG[1]
GRCh37.p13 chr 1 NC_000001.10:g.145706731AGC[1]
Gene: CD160, CD160 molecule (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CD160 transcript variant 1 NM_007053.4:c.24CTG[1] CC [TGCT] > C [TGT] Coding Sequence Variant
CD160 antigen precursor NP_008984.1:p.Cys10del CC (CysCys) > C (Cys) Inframe Deletion
CD160 transcript variant 2 NR_103845.2:n. N/A Intron Variant
CD160 transcript variant X1 XM_011509104.3:c.24CTG[1] CC [TGCT] > C [TGT] Coding Sequence Variant
CD160 antigen isoform X1 XP_011507406.1:p.Cys10del CC (CysCys) > C (Cys) Inframe Deletion
CD160 transcript variant X2 XM_005272929.4:c.24CTG[1] CC [TGCT] > C [TGT] Coding Sequence Variant
CD160 antigen isoform X1 XP_005272986.1:p.Cys10del CC (CysCys) > C (Cys) Inframe Deletion
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 (GCT)2G= delCTG
GRCh38.p14 chr 1 NC_000001.11:g.145728350_145728356= NC_000001.11:g.145728351CTG[1]
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.2543763_2543769= NW_003871055.3:g.2543764CTG[1]
GRCh37.p13 chr 1 NC_000001.10:g.145706730_145706736= NC_000001.10:g.145706731AGC[1]
CD160 transcript variant X2 XM_005272929.4:c.23_29= XM_005272929.4:c.24CTG[1]
CD160 transcript variant X2 XM_005272929.3:c.23_29= XM_005272929.3:c.24CTG[1]
CD160 transcript variant X2 XM_005272929.2:c.23_29= XM_005272929.2:c.24CTG[1]
CD160 transcript variant X1 XM_005272929.1:c.23_29= XM_005272929.1:c.24CTG[1]
CD160 transcript variant 1 NM_007053.4:c.23_29= NM_007053.4:c.24CTG[1]
CD160 transcript variant 1 NM_007053.3:c.23_29= NM_007053.3:c.24CTG[1]
CD160 transcript variant X1 XM_011509104.3:c.23_29= XM_011509104.3:c.24CTG[1]
CD160 transcript variant X1 XM_011509104.2:c.23_29= XM_011509104.2:c.24CTG[1]
CD160 transcript variant X1 XM_011509104.1:c.23_29= XM_011509104.1:c.24CTG[1]
CD160 antigen isoform X1 XP_005272986.1:p.Gly8_Cys10= XP_005272986.1:p.Cys10del
CD160 antigen precursor NP_008984.1:p.Gly8_Cys10= NP_008984.1:p.Cys10del
CD160 antigen isoform X1 XP_011507406.1:p.Gly8_Cys10= XP_011507406.1:p.Cys10del
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#.

6 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 WARNICH_LAB ss678270350 Apr 25, 2013 (138)
2 EVA_EXAC ss1711633101 Apr 09, 2015 (144)
3 GNOMAD ss2731793336 Oct 11, 2018 (152)
4 GNOMAD ss4002400572 Apr 25, 2021 (155)
5 TOPMED ss4466394198 Apr 25, 2021 (155)
6 HUGCELL_USP ss5444750021 Oct 12, 2022 (156)
7 ExAC NC_000001.10 - 145706730 Oct 11, 2018 (152)
8 gnomAD - Genomes NC_000001.11 - 145728350 Apr 25, 2021 (155)
9 gnomAD - Exomes NC_000001.10 - 145706730 Jul 12, 2019 (153)
10 TopMed NC_000001.11 - 145728350 Apr 25, 2021 (155)
11 ALFA NC_000001.11 - 145728350 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
4952947, 812884, ss678270350, ss1711633101, ss2731793336 NC_000001.10:145706729:CAG: NC_000001.11:145728349:GCTGCTG:GCTG (self)
25380353, 30000533, ss4002400572, ss4466394198, ss5444750021 NC_000001.11:145728349:GCT: NC_000001.11:145728349:GCTGCTG:GCTG (self)
2052384618 NC_000001.11:145728349:GCTGCTG:GCTG NC_000001.11:145728349:GCTGCTG:GCTG (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 rs377407780

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