Skip to main page content

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
chr8:60850486 (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.

G>A / G>T
Variation Type
SNV Single Nucleotide Variation
T=0.00000 (1/244732, GnomAD)
T=0.00002 (2/114788, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CHD7 : Intron Variant
7 citations
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 8 NC_000008.11:g.60850486G>A
GRCh38.p7 chr 8 NC_000008.11:g.60850486G>T
GRCh37.p13 chr 8 NC_000008.10:g.61763045G>A
GRCh37.p13 chr 8 NC_000008.10:g.61763045G>T
CHD7 RefSeqGene (LRG_176) NG_007009.1:g.176707G>A
CHD7 RefSeqGene (LRG_176) NG_007009.1:g.176707G>T
Gene: CHD7, chromodomain helicase DNA binding protein 7 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHD7 transcript variant 2 NM_001316690.1:c. N/A Intron Variant
CHD7 transcript variant 1 NM_017780.3:c. N/A Intron Variant
CHD7 transcript variant X1 XM_011517553.2:c. N/A Intron Variant
CHD7 transcript variant X2 XM_011517554.2:c. N/A Intron Variant
CHD7 transcript variant X4 XM_011517555.2:c. N/A Intron Variant
CHD7 transcript variant X3 XM_017013612.1:c. N/A Intron Variant
CHD7 transcript variant X5 XM_017013613.1:c. N/A Intron Variant
CHD7 transcript variant X6 XM_011517560.2:c. N/A Genic Downstream Transcript Variant

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: A (allele ID: 101692 )
ClinVar Accession Disease Names Clinical Significance
RCV000081841.5 not provided Pathogenic
RCV000176678.3 CHARGE association 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 244732 G=1.00000 T=0.00000
The Genome Aggregation Database European Sub 132910 G=0.99999 T=0.00001
The Genome Aggregation Database Asian Sub 47840 G=1.0000 T=0.0000
The Genome Aggregation Database American Sub 33464 G=1.0000 T=0.0000
The Genome Aggregation Database African Sub 15234 G=1.0000 T=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9826 G=1.000 T=0.000
The Genome Aggregation Database Other Sub 5458 G=1.000 T=0.000
The Exome Aggregation Consortium Global Study-wide 114788 G=0.99998 T=0.00002
The Exome Aggregation Consortium Europe Sub 70158 G=1.0000 T=0.0000
The Exome Aggregation Consortium Asian Sub 23584 G=1.0000 T=0.0000
The Exome Aggregation Consortium American Sub 10880 G=1.0000 T=0.0000
The Exome Aggregation Consortium African Sub 9316 G=1.000 T=0.000
The Exome Aggregation Consortium Other Sub 850 G=1.00 T=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 G= A T Note
GRCh38.p7 chr 8 NC_000008.11:g.60...






GRCh37.p13 chr 8 NC_000008.10:g.61...






CHD7 RefSeqGene (LRG_176) NG_007009.1:g.176...







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#.

2 Frequency, 3 SubSNP, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGL ss947848236 Jan 23, 2014 (138)
2 EVA_EXAC ss1689209141 Apr 01, 2015 (144)
3 GNOMAD ss2737175753 Nov 08, 2017 (151)
4 The Exome Aggregation Consortium NC_000008.10 - 61763045 Jul 20, 2018 (151)
5 The Genome Aggregation Database NC_000008.10 - 61763045 Jul 20, 2018 (151)
6 ClinVar RCV000081841.5 Jul 20, 2018 (151)
7 ClinVar RCV000176678.3 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
9310235, 6190488, ss1689209141, ss2737175753 NC_000008.10:61763044:G= NC_000008.11:60850485:G= (self)
ss947848236 NC_000008.11:60850485:G= NC_000008.11:60850485:G= (self)
RCV000081841.5, RCV000176678.3, ss947848236 NC_000008.11:60850485:G>A NC_000008.11:60850485:G>A (self)
9310235, 6190488, ss1689209141, ss2737175753 NC_000008.10:61763044:G>T NC_000008.11:60850485:G>T (self)

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

7 citations for rs398124321
PMID Title Author Year Journal
15300250 Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Vissers LE et al. 2004 Nature genetics
16155193 CHARGE syndrome: the phenotypic spectrum of mutations in the CHD7 gene. Jongmans MC et al. 2006 Journal of medical genetics
16615981 Phenotypic spectrum of CHARGE syndrome with CHD7 mutations. Aramaki M et al. 2006 The Journal of pediatrics
21158681 Mutations in the CHD7 gene: the experience of a commercial laboratory. Bartels CF et al. 2010 Genetic testing and molecular biomarkers
21931733 CHD7 mutational analysis and clinical considerations for auditory rehabilitation in deaf patients with CHARGE syndrome. Song MH et al. 2011 PloS one
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 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