NM_001105206.3(LAMA4):c.195+144T>C AND not specified

Germline classification:: Benign (4 submissions)
Last evaluated:: May 9, 2015
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:: RCV000150907.9

Allele description [Variation Report for NM_001105206.3(LAMA4):c.195+144T>C]

NM_001105206.3(LAMA4):c.195+144T>C

Genes:

LAMA4-AS1:LAMA4 antisense RNA 1 [Gene - HGNC]
LAMA4:laminin subunit alpha 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q21

Genomic location:

Preferred name:

NM_001105206.3(LAMA4):c.195+144T>C

HGVS:

NC_000006.12:g.112253812A>G
NG_008209.1:g.5815T>C
NM_001105206.3:c.195+144T>CMANE SELECT
NM_001105207.3:c.195+144T>C
NM_001105208.3:c.339T>C
NM_001105209.3:c.339T>C
NM_002290.5:c.195+144T>C
NP_001098678.1:p.Leu113=
NP_001098679.1:p.Leu113=
NP_001098679.1:p.Leu113=
LRG_433t2:c.195+144T>C
LRG_433:g.5815T>C
NC_000006.11:g.112575014A>G
NM_001105209.1:c.339T>C
NM_001105209.2:c.339T>C
NM_002290.3:c.195+144T>C
p.Leu113Leu

Links:

dbSNP: rs147118520

NCBI 1000 Genomes Browser:

rs147118520

Molecular consequence:

NM_001105206.3:c.195+144T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001105207.3:c.195+144T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_002290.5:c.195+144T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001105208.3:c.339T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001105209.3:c.339T>C - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000198512	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Nov 10, 2011)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000516556	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (May 9, 2015)	germline	clinical testing	Citation Link,
SCV001922966	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV001975592	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing

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	3	3	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 Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000198512.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	PubMed (1)

Description

Leu113Leu in Exon 02 of LAMA4: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue, is not located within the splice consensus sequence and has been identified in 1.4% (99/6950) of Euro pean American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs147118520).

#	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		3	not provided	3	not provided

From GeneDx, SCV000516556.4

#	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

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001922966.1

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001975592.1

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

Last Updated: Oct 13, 2024

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