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

Clinical significance:Benign (Last evaluated: Jun 27, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

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

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

CHD7:chromodomain helicase DNA binding protein 7 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_017780.4(CHD7):c.309G>A (p.Ser103=)
  • 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.(=)
dbSNP: rs115293759
NCBI 1000 Genomes Browser:
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]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000699436Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
(Jun 27, 2016)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Summary from all submissions

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



Unique phenotype in a patient with CHARGE syndrome.

Jain S, Kim HG, Lacbawan F, Meliciani I, Wenzel W, Kurth I, Sharma J, Schoeneman M, Ten S, Layman LC, Jacobson-Dickman E.

Int J Pediatr Endocrinol. 2011 Oct 13;2011:11. doi: 10.1186/1687-9856-2011-11.

PubMed [citation]

Mutation update on the CHD7 gene involved in CHARGE syndrome.

Janssen N, Bergman JE, Swertz MA, Tranebjaerg L, Lodahl M, Schoots J, Hofstra RM, van Ravenswaaij-Arts CM, Hoefsloot LH.

Hum Mutat. 2012 Aug;33(8):1149-60. doi: 10.1002/humu.22086. Epub 2012 Apr 16. Review.

PubMed [citation]
See all PubMed Citations (4)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699436.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)


Variant summary: The CHD7 c.309G>A (p.Ser103Ser) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant, but 5/5 splicing algorithms predict no significant change to normal splicing. This variant was found in 199/119626 control chromosomes (3 homozygotes) at a frequency of 0.0016635, which is approximately 1331 times the estimated maximal expected allele frequency of a pathogenic CHD7 variant (0.0000013), suggesting this variant is likely a benign polymorphism. The variant has been cited in at least one CHARGE syndrome patient in the literature without evidence of causality (Jain_Int J Pediatr Endocrinol_2011). In addition, one clinical diagnostic laboratory classified this variant as benign. Based on the synonymous nature of this variant and the high allele frequency in the general population, this variant was classified as benign.

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

Last Updated: Sep 24, 2021

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