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NM_017780.4(CHD7):c.4534-13T>G

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(6);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 28, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000158297.7
Variation ID:
158297
Description:
single nucleotide variant
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NM_017780.4(CHD7):c.4534-13T>G

Allele ID
168613
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8q12.2
Genomic location
8: 60841631 (GRCh38) GRCh38 UCSC
8: 61754190 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_176t1:c.4534-13T>G
LRG_176:g.167852T>G
NC_000008.10:g.61754190T>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000008.11:60841630:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.01318 (G)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00325
1000 Genomes Project 0.01318
The Genome Aggregation Database (gnomAD) 0.00946
Trans-Omics for Precision Medicine (TOPMed) 0.01114
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01119
The Genome Aggregation Database (gnomAD), exomes 0.00259
Links
ClinGen: CA201802
dbSNP: rs114996731
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Aug 23, 2017 RCV000176104.3
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Aug 11, 2017 RCV000514439.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000353027.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 7, 2020 RCV000145672.5
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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
1711 1739

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: SCV000192774.1
Submitted: (Sep 11, 2014)
Evidence details
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000312974.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Oct 28, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000227702.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
http://www.ncbi.nlm.nih.gov/vari…
Likely benign
(Aug 11, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000609930.1
Submitted: (Oct 05, 2017)
Evidence details
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: SCV000967056.1
Submitted: (Mar 21, 2019)
Evidence details
Comment:
c.4534-13T>G in intron 19 of CHD7: This variant is not expected to have clinical significance because it has been identified in 3.79% (370/9758) of African … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Kallmann Syndrome 5
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000474437.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
CHARGE association
Allele origin: germline
Invitae
Accession: SCV001723821.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001946035.1
Submitted: (Sep 28, 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.

Text-mined citations for rs114996731...

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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 Oct 30, 2021