NM_004006.3(DMD):c.7427A>G (p.Asn2476Ser) AND not specified

Germline classification:: Likely benign (1 submission)
Last evaluated:: Feb 25, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001174938.1

Allele description [Variation Report for NM_004006.3(DMD):c.7427A>G (p.Asn2476Ser)]

NM_004006.3(DMD):c.7427A>G (p.Asn2476Ser)

Gene:

DMD:dystrophin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp21.1

Genomic location:

Preferred name:

NM_004006.3(DMD):c.7427A>G (p.Asn2476Ser)

HGVS:

NC_000023.11:g.31774075T>C
NG_012232.1:g.1570535A>G
NM_000109.4:c.7403A>G
NM_004006.3:c.7427A>GMANE SELECT
NM_004009.3:c.7415A>G
NM_004010.3:c.7058A>G
NM_004011.4:c.3404A>G
NM_004012.4:c.3395A>G
NM_004013.3:c.47A>G
NM_004020.4:c.47A>G
NM_004021.3:c.47A>G
NM_004022.3:c.47A>G
NM_004023.3:c.47A>G
NP_000100.3:p.Asn2468Ser
NP_003997.1:p.Asn2476Ser
NP_003997.2:p.Asn2476Ser
NP_004000.1:p.Asn2472Ser
NP_004001.1:p.Asn2353Ser
NP_004002.3:p.Asn1135Ser
NP_004003.2:p.Asn1132Ser
NP_004004.2:p.Asn16Ser
NP_004011.3:p.Asn16Ser
NP_004012.2:p.Asn16Ser
NP_004013.2:p.Asn16Ser
NP_004014.2:p.Asn16Ser
LRG_199t1:c.7427A>G
LRG_199:g.1570535A>G
LRG_199p1:p.Asn2476Ser
NC_000023.10:g.31792192T>C
NM_004006.2:c.7427A>G

Protein change:

N1132S

Links:

dbSNP: rs757394130

NCBI 1000 Genomes Browser:

rs757394130

Molecular consequence:

NM_000109.4:c.7403A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004006.3:c.7427A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004009.3:c.7415A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004010.3:c.7058A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004011.4:c.3404A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004012.4:c.3395A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004013.3:c.47A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004020.4:c.47A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004021.3:c.47A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004022.3:c.47A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004023.3:c.47A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Homo sapiens zinc finger protein 169, mRNA (cDNA clone IMAGE:3863569), complete cds
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001338389	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Feb 25, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001338389

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(Feb 25, 2020)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001338389.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Variant summary: DMD c.7427A>G (p.Asn2476Ser) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 9.3e-05 in 183247 control chromosomes (gnomAD). The observed variant frequency is approximately 8.4- fold the estimated maximal expected allele frequency for a pathogenic variant in DMD causing Dystrophinopathies phenotype (1.1e-05), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.7427A>G in individuals affected with Dystrophinopathies and no experimental evidence demonstrating its impact on protein function have been reported. Two other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as benign, and one laboratory classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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