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dbSNP Short Genetic Variations

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.


Current Build 151

Released July 17, 2018

Homo sapiens
chr10:49461382-49461383 (GRCh38.p7) 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.

Variation Type
delCT=0.00002 (5/246010, GnomAD)
delCT=0.00002 (2/125568, TOPMED)
delCT=0.00001 (1/121090, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ERCC6 : Frameshift
1 citation
Genomic View
See rs on genome

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.p7 chr 10 NC_000010.11:g.49461382_49461383delCT
GRCh37.p13 chr 10 NC_000010.10:g.50669428_50669429delCT
ERCC6 RefSeqGene (LRG_465) NG_009442.1:g.82719_82720delAG
Gene: ERCC6, excision repair cross-complementation group 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ERCC6 transcript variant 1 NM_001277058.1:c. N/A Genic Downstream Transcript Variant
ERCC6 transcript variant 2 NM_001277059.1:c. N/A Genic Downstream Transcript Variant
ERCC6 transcript variant 3 NM_000124.3:c.395...


R [AGG] > G [G] Coding Sequence Variant
DNA excision repair protein ERCC-6 isoform 2 NP_000115.1:p.Arg...


R (Arg) > G (Gly) Frameshift

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.

Allele: delCT (allele ID: 187988 )
ClinVar Accession Disease Names Clinical Significance
RCV000170390.1 Cockayne syndrome B Likely-Pathogenic

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").

Study Population Group Sample Size Ref Allele Alt Allele
The Genome Aggregation Database Global Study-wide 246010 CT=0.99998 delCT=0.00002
The Genome Aggregation Database European Sub 133774 CT=0.99996 delCT=0.00004
The Genome Aggregation Database Asian Sub 48026 CT=1.0000 delCT=0.0000
The Genome Aggregation Database American Sub 33580 CT=1.0000 delCT=0.0000
The Genome Aggregation Database African Sub 15302 CT=1.0000 delCT=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9846 CT=1.000 delCT=0.000
The Genome Aggregation Database Other Sub 5482 CT=1.000 delCT=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 CT=0.99998 delCT=0.00002
The Exome Aggregation Consortium Global Study-wide 121090 CT=0.99999 delCT=0.00001
The Exome Aggregation Consortium Europe Sub 73158 CT=1.0000 delCT=0.0000
The Exome Aggregation Consortium Asian Sub 25112 CT=1.0000 delCT=0.0000
The Exome Aggregation Consortium American Sub 11544 CT=1.0000 delCT=0.0000
The Exome Aggregation Consortium African Sub 10374 CT=1.0000 delCT=0.0000
The Exome Aggregation Consortium Other Sub 902 CT=1.00 delCT=0.00

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 CT= delCT Note
GRCh38.p7 chr 10 NC_000010.11:g.49461382...




GRCh37.p13 chr 10 NC_000010.10:g.50669428...




ERCC6 RefSeqGene (LRG_465) NG_009442.1:g.82719_827...




ERCC6 transcript variant 3 NM_000124.3:c.3952_3953AG= NM_000124.3:c.3952_3953...


DNA excision repair protein ERCC-6 isoform 2 NP_000115.1:p.Arg1318= NP_000115.1:p.Arg1318fs

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#.

3 Frequency, 5 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1711937467 Apr 01, 2015 (144)
2 CLINVAR ss1751119411 May 21, 2015 (144)
3 TOPMED ss2337557072 Dec 20, 2016 (150)
4 GNOMAD ss2738241140 Nov 08, 2017 (151)
5 TOPMED ss3119238427 Nov 08, 2017 (151)
6 The Exome Aggregation Consortium NC_000010.10 - 50669428 Jul 20, 2018 (151)
7 The Genome Aggregation Database NC_000010.10 - 50669428 Jul 20, 2018 (151)
8 Trans-Omics for Precision Medicine NC_000010.11 - 49461382 Jul 20, 2018 (151)
9 ClinVar RCV000170390.1 Jul 20, 2018 (151)

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
118329, 7255875, ss1711937467, ss2337557072, ss2738241140 NC_000010.10:50669427:CT= NC_000010.11:49461381:CT= (self)
42178607, ss1751119411, ss3119238427 NC_000010.11:49461381:CT= NC_000010.11:49461381:CT= (self)
118329, 7255875, ss1711937467, ss2337557072, ss2738241140 NC_000010.10:50669427:delCT NC_000010.11:49461381:delCT (self)
RCV000170390.1, 42178607, ss1751119411, ss3119238427 NC_000010.11:49461381:delCT NC_000010.11:49461381:delCT (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs765825423
PMID Title Author Year Journal
18414213 ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Richards CS et al. 2008 Genetics in medicine

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: 0.1.4.post833+d3ba21e