6-129280072-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM5BP4_StrongBS2
The NM_000426.4(LAMA2):c.2462C>T(p.Thr821Met) variant causes a missense change. The variant allele was found at a frequency of 0.0023 in 1,612,224 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T821P) has been classified as Pathogenic.
Frequency
Consequence
NM_000426.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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LAMA2 | ENST00000421865.3 | c.2462C>T | p.Thr821Met | missense_variant | Exon 18 of 65 | 5 | NM_000426.4 | ENSP00000400365.2 | ||
LAMA2 | ENST00000618192.5 | c.2462C>T | p.Thr821Met | missense_variant | Exon 18 of 66 | 5 | ENSP00000480802.2 | |||
LAMA2 | ENST00000617695.5 | c.2462C>T | p.Thr821Met | missense_variant | Exon 18 of 64 | 5 | ENSP00000481744.2 |
Frequencies
GnomAD3 genomes AF: 0.00168 AC: 256AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00193 AC: 485AN: 251274Hom.: 2 AF XY: 0.00183 AC XY: 248AN XY: 135788
GnomAD4 exome AF: 0.00237 AC: 3457AN: 1459934Hom.: 10 Cov.: 30 AF XY: 0.00231 AC XY: 1676AN XY: 726406
GnomAD4 genome AF: 0.00167 AC: 255AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.00158 AC XY: 118AN XY: 74466
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
LAMA2: PM5, BP4, BS2 -
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This variant is associated with the following publications: (PMID: 24611677, 24082139, 27896284, 23891399) -
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not specified Uncertain:1Benign:1
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Variant summary: LAMA2 c.2462C>T (p.Thr821Met) results in a non-conservative amino acid change located in the EGF-like domain (IPR000742) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.002 in 282674 control chromosomes, predominantly at a frequency of 0.0036 within the Finnish subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within Finnish control individuals in the gnomAD database is approximately two fold of the estimated maximal expected allele frequency for a pathogenic variant in LAMA2 causing Laminin Alpha 2-Related Dystrophy phenotype (0.0022), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Finnish origin. c.2462C>T has been reported in the literature in at least two homozygous individuals affected with Laminin Alpha 2-Related Dystrophy (example Xiong_2015, Ge_2019, Tan_2021). However, these reports do not provide unequivocal evidence for an association of the variant with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Eight clinical-significance assessments for this variant have been submitted to ClinVar after 2014 with conflicting assessments (VUS n=5, likely benign n=2, benign n=1). Based on the evidence outlined above, the variant was classified as likely benign. -
Merosin deficient congenital muscular dystrophy Uncertain:1
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Congenital muscular dystrophy due to partial LAMA2 deficiency Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Merosin deficient congenital muscular dystrophy;C4748327:Muscular dystrophy, limb-girdle, autosomal recessive 23 Uncertain:1
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LAMA2-related muscular dystrophy Benign:1
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Intellectual disability Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at