Variant rs372962551 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000426.4(LAMA2):c.3175-32_3175-31delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,371,902 control chromosomes in the GnomAD database, including 10,107 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1235 hom., cov: 31)

Exomes 𝑓: 0.10 ( 8872 hom. )

Consequence

LAMA2
NM_000426.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0980

Variant links:

Genes affected

LAMA2 (HGNC:6482): (laminin subunit alpha 2) Laminin, an extracellular protein, is a major component of the basement membrane. It is thought to mediate the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. It is composed of three subunits, alpha, beta, and gamma, which are bound to each other by disulfide bonds into a cross-shaped molecule. This gene encodes the alpha 2 chain, which constitutes one of the subunits of laminin 2 (merosin) and laminin 4 (s-merosin). Mutations in this gene have been identified as the cause of congenital merosin-deficient muscular dystrophy. Two transcript variants encoding different proteins have been found for this gene. [provided by RefSeq, Jul 2008]

LAMA2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 6-129312825-TTG-T is Benign according to our data. Variant chr6-129312825-TTG-T is described in ClinVar as [Benign]. Clinvar id is 256066.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-129312825-TTG-T is described in Lovd as [Benign]. Variant chr6-129312825-TTG-T is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LAMA2	NM_000426.4 linkuse as main transcript	c.3175-32_3175-31delGT		intron_variant		ENST00000421865.3	NP_000417.3
LAMA2	NM_001079823.2 linkuse as main transcript	c.3175-32_3175-31delGT		intron_variant			NP_001073291.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
LAMA2	ENST00000421865.3 linkuse as main transcript	c.3175-32_3175-31delGT	intron_variant	5	NM_000426.4	ENSP00000400365.2	P24043
LAMA2	ENST00000618192.5 linkuse as main transcript	c.3439-32_3439-31delGT	intron_variant	5		ENSP00000480802.2	A0A087WX80
LAMA2	ENST00000617695.5 linkuse as main transcript	c.3175-32_3175-31delGT	intron_variant	5		ENSP00000481744.2	A0A087WYF1

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16165

AN:

152080

Hom.:

1233

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0779

Gnomad AMI

AF:

0.0735

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.0956

Gnomad EAS

AF:

0.390

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.0795

Gnomad OTH

AF:

0.112

GnomAD3 exomes

AF:

0.135

AC:

33557

AN:

247754

Hom.:

3431

AF XY:

0.128

AC XY:

17122

AN XY:

134234

show subpopulations

Gnomad AFR exome

AF:

0.0747

Gnomad AMR exome

AF:

0.274

Gnomad ASJ exome

AF:

0.0954

Gnomad EAS exome

AF:

0.388

Gnomad SAS exome

AF:

0.0974

Gnomad FIN exome

AF:

0.123

Gnomad NFE exome

AF:

0.0776

Gnomad OTH exome

AF:

0.126

GnomAD4 exome

AF:

0.102

AC:

124733

AN:

1219704

Hom.:

8872

AF XY:

0.101

AC XY:

62622

AN XY:

619320

show subpopulations

Gnomad4 AFR exome

AF:

0.0785

Gnomad4 AMR exome

AF:

0.266

Gnomad4 ASJ exome

AF:

0.0978

Gnomad4 EAS exome

AF:

0.386

Gnomad4 SAS exome

AF:

0.0954

Gnomad4 FIN exome

AF:

0.124

Gnomad4 NFE exome

AF:

0.0814

Gnomad4 OTH exome

AF:

0.112

GnomAD4 genome

AF:

0.106

AC:

16172

AN:

152198

Hom.:

1235

Cov.:

AF XY:

0.112

AC XY:

8301

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0778

Gnomad4 AMR

AF:

0.203

Gnomad4 ASJ

AF:

0.0956

Gnomad4 EAS

AF:

0.391

Gnomad4 SAS

AF:

0.103

Gnomad4 FIN

AF:

0.118

Gnomad4 NFE

AF:

0.0795

Gnomad4 OTH

AF:

0.111

Alfa

AF:

0.0944

Hom.:

153

Bravo

AF:

0.116

Asia WGS

AF:

0.196

AC:

682

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 27, 2016	- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 20, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over