rs144492513
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_000426.4(LAMA2):c.2767G>A(p.Gly923Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000415 in 1,613,786 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G923G) has been classified as Likely benign.
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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.2767G>A | p.Gly923Ser | missense_variant | 20/65 | ENST00000421865.3 | |
LAMA2 | NM_001079823.2 | c.2767G>A | p.Gly923Ser | missense_variant | 20/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.2767G>A | p.Gly923Ser | missense_variant | 20/65 | 5 | NM_000426.4 | ||
LAMA2 | ENST00000618192.5 | c.2767G>A | p.Gly923Ser | missense_variant | 20/66 | 5 | P1 | ||
LAMA2 | ENST00000617695.5 | c.2767G>A | p.Gly923Ser | missense_variant | 20/64 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251418Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135888
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461500Hom.: 1 Cov.: 30 AF XY: 0.0000316 AC XY: 23AN XY: 727076
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74462
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 06, 2021 | In silico analysis supports that this missense variant does not alter protein structure/function; Previously reported in an individual with dilated cardiomyopathy, however detailed clinical information was not provided (Mazzarotto et al., 2020); This variant is associated with the following publications: (PMID: 31983221, 30055037) - |
LAMA2-related muscular dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at