20-62330822-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005560.6(LAMA5):āc.3773T>Gā(p.Met1258Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000717 in 1,395,390 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M1258T) has been classified as Benign.
Frequency
Consequence
NM_005560.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA5 | NM_005560.6 | c.3773T>G | p.Met1258Arg | missense_variant | 30/80 | ENST00000252999.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA5 | ENST00000252999.7 | c.3773T>G | p.Met1258Arg | missense_variant | 30/80 | 1 | NM_005560.6 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 7.17e-7 AC: 1AN: 1395390Hom.: 0 Cov.: 63 AF XY: 0.00 AC XY: 0AN XY: 688114
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at