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

Clinical significance:Benign/Likely benign (Last evaluated: Dec 2, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000458054.6

Allele description [Variation Report for NM_017780.4(CHD7):c.6478G>A (p.Ala2160Thr)]

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

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.6478G>A (p.Ala2160Thr)
Other names:
NM_017780.3(CHD7):c.6478G>A(p.Ala2160Thr)
HGVS:
  • NC_000008.11:g.60853203G>A
  • NG_007009.1:g.179424G>A
  • NM_001316690.1:c.1717-9026G>A
  • NM_017780.4:c.6478G>AMANE SELECT
  • NP_060250.2:p.Ala2160Thr
  • LRG_176t1:c.6478G>A
  • LRG_176:g.179424G>A
  • NC_000008.10:g.61765762G>A
  • NM_017780.2:c.6478G>A
  • NM_017780.3:c.6478G>A
  • Q9P2D1:p.Ala2160Thr
Protein change:
A2160T
Links:
UniProtKB: Q9P2D1#VAR_068146; dbSNP: rs61753399
NCBI 1000 Genomes Browser:
rs61753399
Molecular consequence:
  • NM_001316690.1:c.1717-9026G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_017780.4:c.6478G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
CHARGE association (CHARGE)
Synonyms:
CHARGE ASSOCIATION--COLOBOMA, HEART ANOMALY, CHOANAL ATRESIA, RETARDATION, GENITAL AND EAR ANOMALIES; CHARGE syndrome; Coloboma, heart anomaly, choanal atresia, retardation, genital and ear anomalies; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008965; MedGen: C0265354; Orphanet: 138; OMIM: 214800

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000562413Invitaecriteria provided, single submitter
Benign
(Dec 2, 2020)
germlineclinical testing

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

SCV000803586SIB Swiss Institute of Bioinformaticscriteria provided, single submitter
Likely benign
(May 31, 2018)
unknowncuration

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

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

Details of each submission

From Invitae, SCV000562413.6

#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 SIB Swiss Institute of Bioinformatics, SCV000803586.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

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 a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age. BP4 => Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.).

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

Last Updated: Sep 6, 2021

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