NM_017780.4(CHD7):c.2835+8T>C AND not provided

Clinical significance:Benign (Last evaluated: Jan 4, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000589620.4

Allele description [Variation Report for NM_017780.4(CHD7):c.2835+8T>C]

NM_017780.4(CHD7):c.2835+8T>C

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.2835+8T>C
HGVS:
  • NC_000008.11:g.60821935T>C
  • NG_007009.1:g.148156T>C
  • NM_001316690.1:c.1717-40294T>C
  • NM_017780.4:c.2835+8T>CMANE SELECT
  • LRG_176:g.148156T>C
  • NC_000008.10:g.61734494T>C
  • NM_017780.3:c.2835+8T>C
Links:
dbSNP: rs202141372
NCBI 1000 Genomes Browser:
rs202141372
Molecular consequence:
  • NM_001316690.1:c.1717-40294T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_017780.4:c.2835+8T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000699435Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Jan 4, 2016)
germlineclinical testing

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

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001791215GeneDxno assertion criteria provided
Likely benign
(Dec 25, 2019)
germlineclinical testing

Citation Link

Summary from all submissions

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

Citations

PubMed

Functionally compromised CHD7 alleles in patients with isolated GnRH deficiency.

Balasubramanian R, Choi JH, Francescatto L, Willer J, Horton ER, Asimacopoulos EP, Stankovic KM, Plummer L, Buck CL, Quinton R, Nebesio TD, Mericq V, Merino PM, Meyer BF, Monies D, Gusella JF, Al Tassan N, Katsanis N, Crowley WF Jr.

Proc Natl Acad Sci U S A. 2014 Dec 16;111(50):17953-8. doi: 10.1073/pnas.1417438111. Epub 2014 Dec 3.

PubMed [citation]
PMID:
25472840
PMCID:
PMC4273325

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699435.1

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

Description

Variant summary: The variant of interest is located at a non-conserved intronic position, not widely known to affect splicing with 5/5 in silico programs via Alamut predicting no significant effect on splicing, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 69/108302 (1/1569), predominantly in the European (Non-Finnish) cohort, 55/60222 (1/1094), which exceeds the maximum expected allele frequency for a pathogenic CHD7 variant of 1/769230. The variant of interest has been reported in one individual affected with normosmic idiopathic hypogonadotropic hypogonadism via publications. Multiple reputable clinical laboratories have cited the variant with varying classifications: "uncertain significance" or "likely benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.

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

From GeneDx, SCV001791215.1

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

Last Updated: Aug 27, 2021

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