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NM_017780.4(CHD7):c.6478G>A (p.Ala2160Thr)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 2, 2021)
Last evaluated:
Dec 2, 2020
Accession:
VCV000158311.10
Variation ID:
158311
Description:
single nucleotide variant
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NM_017780.4(CHD7):c.6478G>A (p.Ala2160Thr)

Allele ID
168627
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8q12.2
Genomic location
8: 60853203 (GRCh38) GRCh38 UCSC
8: 61765762 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
Q9P2D1:p.Ala2160Thr
NC_000008.11:g.60853203G>A
LRG_176:g.179424G>A
... more HGVS
Protein change
A2160T
Other names
NM_017780.3(CHD7):c.6478G>A(p.Ala2160Thr)
Canonical SPDI
NC_000008.11:60853202:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00439 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00462
Exome Aggregation Consortium (ExAC) 0.00127
Trans-Omics for Precision Medicine (TOPMed) 0.00472
The Genome Aggregation Database (gnomAD), exomes 0.00105
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00392
1000 Genomes Project 0.00439
Links
ClinGen: CA171759
UniProtKB: Q9P2D1#VAR_068146
dbSNP: rs61753399
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 5 criteria provided, multiple submitters, no conflicts Aug 23, 2017 RCV000145686.7
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 2, 2020 RCV000458054.6
Benign 1 criteria provided, single submitter Jul 1, 2016 RCV000716492.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CHD7 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1584 1612

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Feb 08, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000192792.1
Submitted: (Sep 11, 2014)
Evidence details
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000312992.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Apr 22, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000512581.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(May 31, 2018)
criteria provided, single submitter
Method: curation
CHARGE association
Allele origin: unknown
SIB Swiss Institute of Bioinformatics
Accession: SCV000803586.1
Submitted: (Jun 13, 2018)
Evidence details
Comment:
This variant is interpreted as a Likely Benign, for CHARGE syndrome, in Autosomal Dominant manner. The following ACMG Tag(s) were applied: BS2 => Observed in … (more)
Benign
(Aug 23, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV001365641.1
Submitted: (May 14, 2020)
Evidence details
Comment:
p.Ala2160Thr in exon 31 of CHD7: This variant is not expected to have clinical significance because it has been identified in 1.47% (140/9514) of African … (more)
Benign
(Jul 01, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000847333.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Benign
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
CHARGE association
Allele origin: germline
Invitae
Accession: SCV000562413.6
Submitted: (Jan 07, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001744917.3
Submitted: (Sep 02, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs61753399...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 07, 2021