NM_017780.4(CHD7):c.309G>A (p.Ser103=) AND not specified

Clinical significance:Benign/Likely benign (Last evaluated: Aug 23, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000081829.8

Allele description [Variation Report for NM_017780.4(CHD7):c.309G>A (p.Ser103=)]

NM_017780.4(CHD7):c.309G>A (p.Ser103=)

Gene:
CHD7:chromodomain helicase DNA binding protein 7 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8q12.2
Genomic location:
Preferred name:
NM_017780.4(CHD7):c.309G>A (p.Ser103=)
HGVS:
  • NC_000008.11:g.60741741G>A
  • NG_007009.1:g.67962G>A
  • NM_001316690.1:c.309G>A
  • NM_017780.4:c.309G>AMANE SELECT
  • NP_001303619.1:p.Ser103=
  • NP_060250.2:p.Ser103=
  • LRG_176t1:c.309G>A
  • LRG_176:g.67962G>A
  • LRG_176p1:p.(=)
  • NC_000008.10:g.61654300G>A
  • NM_017780.2:c.309G>A
  • NM_017780.3:c.309G>A
  • NP_060250.2:p.(=)
Links:
dbSNP: rs115293759
NCBI 1000 Genomes Browser:
rs115293759
Molecular consequence:
  • NM_001316690.1:c.309G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_017780.4:c.309G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000113764EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Benign
(Sep 26, 2013)
germlineclinical testing

Citation Link,

SCV000312968PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Likely benigngermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000512577GeneDxcriteria provided, single submitter
Benign
(Apr 22, 2016)
germlineclinical testing

Citation Link,

SCV001365640Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Benign
(Aug 23, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown51not providednot providednot providedclinical testing

Citations

PubMed

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, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000113764.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided4not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided4not providednot providednot provided

From PreventionGenetics,PreventionGenetics, SCV000312968.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV000512577.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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 a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV001365640.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

p.Ser103Ser in exon 2 of CHD7: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 1.89% (183/9668) of African chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs115293759).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not provided1not provided

Last Updated: Jul 7, 2021

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