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GeneBe

6-128981135-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000426.4(LAMA2):c.113-68783T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,052 control chromosomes in the GnomAD database, including 3,450 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.15 ( 3450 hom., cov: 31)

Consequence

LAMA2
NM_000426.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.157
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LAMA2NM_000426.4 linkuse as main transcriptc.113-68783T>C intron_variant ENST00000421865.3
LAMA2NM_001079823.2 linkuse as main transcriptc.113-68783T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LAMA2ENST00000421865.3 linkuse as main transcriptc.113-68783T>C intron_variant 5 NM_000426.4

Frequencies

GnomAD3 genomes
AF:
0.153
AC:
23249
AN:
151932
Hom.:
3447
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.386
Gnomad AMI
AF:
0.0473
Gnomad AMR
AF:
0.0901
Gnomad ASJ
AF:
0.112
Gnomad EAS
AF:
0.00116
Gnomad SAS
AF:
0.157
Gnomad FIN
AF:
0.0459
Gnomad MID
AF:
0.134
Gnomad NFE
AF:
0.0576
Gnomad OTH
AF:
0.141
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.153
AC:
23299
AN:
152052
Hom.:
3450
Cov.:
31
AF XY:
0.151
AC XY:
11212
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.386
Gnomad4 AMR
AF:
0.0900
Gnomad4 ASJ
AF:
0.112
Gnomad4 EAS
AF:
0.00116
Gnomad4 SAS
AF:
0.159
Gnomad4 FIN
AF:
0.0459
Gnomad4 NFE
AF:
0.0576
Gnomad4 OTH
AF:
0.145
Alfa
AF:
0.0735
Hom.:
759
Bravo
AF:
0.164
Asia WGS
AF:
0.0980
AC:
343
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
2.1
Dann
Benign
0.38

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.

Other links and lift over

dbSNP: rs11154452; hg19: chr6-129302280; API