6-128883258-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_000426.4(LAMA2):c.13G>A(p.Ala5Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,555,746 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000426.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000944 AC: 15AN: 158820Hom.: 0 AF XY: 0.000106 AC XY: 9AN XY: 84902
GnomAD4 exome AF: 0.000110 AC: 155AN: 1403540Hom.: 0 Cov.: 31 AF XY: 0.000128 AC XY: 89AN XY: 692952
GnomAD4 genome AF: 0.000138 AC: 21AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74358
ClinVar
Submissions by phenotype
not provided Uncertain:2
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LAMA2-related muscular dystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at