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NM_017780.4(CHD7):c.7590A>G (p.Lys2530=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(4);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Sep 2, 2021)
Last evaluated:
Dec 2, 2020
Accession:
VCV000158318.10
Variation ID:
158318
Description:
single nucleotide variant
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NM_017780.4(CHD7):c.7590A>G (p.Lys2530=)

Allele ID
168634
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8q12.2
Genomic location
8: 60856870 (GRCh38) GRCh38 UCSC
8: 61769429 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_176t1:c.7590A>G
LRG_176:g.183091A>G
NC_000008.10:g.61769429A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000008.11:60856869:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00439 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00475
The Genome Aggregation Database (gnomAD), exomes 0.00122
1000 Genomes Project 0.00439
Exome Aggregation Consortium (ExAC) 0.00141
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00362
The Genome Aggregation Database (gnomAD) 0.00459
Links
ClinGen: CA271337
dbSNP: rs61742801
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 4 criteria provided, multiple submitters, no conflicts Aug 23, 2017 RCV000249926.6
Benign 1 criteria provided, single submitter Jul 1, 2016 RCV000716506.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 2, 2020 RCV000145694.6
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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
1607 1635

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Feb 08, 2013)
criteria provided, single submitter
Method: clinical testing
CHARGE syndrome
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000192802.1
Submitted: (Sep 11, 2014)
Evidence details
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000313000.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Apr 25, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000512585.4
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)
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: SCV001365642.1
Submitted: (May 14, 2020)
Evidence details
Comment:
p.Lys2530Lys in exon 34 of CHD7: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is … (more)
Benign
(Jul 01, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000847347.3
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: SCV000562416.6
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: SCV001743370.3
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 rs61742801...

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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