NM_004006.3(DMD):c.9682T>C (p.Phe3228Leu) AND not specified

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Jul 21, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000217993.11

Allele description [Variation Report for NM_004006.3(DMD):c.9682T>C (p.Phe3228Leu)]

NM_004006.3(DMD):c.9682T>C (p.Phe3228Leu)

Gene:

DMD:dystrophin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp21.2

Genomic location:

Preferred name:

NM_004006.3(DMD):c.9682T>C (p.Phe3228Leu)

HGVS:

NC_000023.11:g.31204086A>G
NG_012232.1:g.2140524T>C
NM_000109.4:c.9658T>C
NM_004006.3:c.9682T>CMANE SELECT
NM_004009.3:c.9670T>C
NM_004010.3:c.9313T>C
NM_004011.4:c.5659T>C
NM_004012.4:c.5650T>C
NM_004013.3:c.2302T>C
NM_004014.3:c.1495T>C
NM_004015.3:c.478T>C
NM_004016.3:c.478T>C
NM_004017.3:c.478T>C
NM_004018.3:c.478T>C
NM_004019.3:c.478T>C
NM_004020.4:c.2302T>C
NM_004021.3:c.2302T>C
NM_004022.3:c.2302T>C
NM_004023.3:c.2302T>C
NP_000100.3:p.Phe3220Leu
NP_003997.1:p.Phe3228Leu
NP_003997.2:p.Phe3228Leu
NP_004000.1:p.Phe3224Leu
NP_004001.1:p.Phe3105Leu
NP_004002.3:p.Phe1887Leu
NP_004003.2:p.Phe1884Leu
NP_004004.2:p.Phe768Leu
NP_004005.2:p.Phe499Leu
NP_004006.1:p.Phe160Leu
NP_004007.1:p.Phe160Leu
NP_004008.1:p.Phe160Leu
NP_004009.1:p.Phe160Leu
NP_004010.1:p.Phe160Leu
NP_004011.3:p.Phe768Leu
NP_004012.2:p.Phe768Leu
NP_004013.2:p.Phe768Leu
NP_004014.2:p.Phe768Leu
LRG_199t1:c.9682T>C
LRG_199:g.2140524T>C
LRG_199p1:p.Phe3228Leu
NC_000023.10:g.31222203A>G
NM_000109.3:c.9658T>C
NM_000109.4:c.9658T>C
NM_004006.2:c.9682T>C

Protein change:

F160L

Links:

dbSNP: rs141392048

NCBI 1000 Genomes Browser:

rs141392048

Molecular consequence:

NM_000109.4:c.9658T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004006.3:c.9682T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004009.3:c.9670T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004010.3:c.9313T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004011.4:c.5659T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004012.4:c.5650T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004013.3:c.2302T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004014.3:c.1495T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004015.3:c.478T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004016.3:c.478T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004017.3:c.478T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004018.3:c.478T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004019.3:c.478T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004020.4:c.2302T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004021.3:c.2302T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004022.3:c.2302T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004023.3:c.2302T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000112757	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Likely benign (Oct 2, 2014)	germline	clinical testing	Citation Link,
SCV000270135	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (Mar 21, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000721717	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jul 21, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000112757

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Likely benign
(Oct 2, 2014)

germline

clinical testing

Citation Link,

SCV000270135

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Likely benign
(Mar 21, 2015)

germline

clinical testing

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

SCV000721717

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(Jul 21, 2017)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	4	4	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Eurofins Ntd Llc (ga), SCV000112757.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

#	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		2	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000270135.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	PubMed (1)

Description

p.Phe3228Leu in exon 67 of DMD: This variant is not expected to have clinical si gnificance because it has been identified in 0.6% (49/8265) of African chromosom es by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; db SNP rs141392048).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		4	not provided	4	not provided

From GeneDx, SCV000721717.1

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

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

Last Updated: Jan 13, 2025

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