chr6-129291619-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000426.4(LAMA2):c.2755C>T(p.Arg919Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000229 in 1,612,964 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R919G) has been classified as Uncertain significance.
Frequency
Consequence
NM_000426.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.2755C>T | p.Arg919Cys | missense_variant | Exon 20 of 65 | 5 | NM_000426.4 | ENSP00000400365.2 | ||
LAMA2 | ENST00000618192.5 | c.2755C>T | p.Arg919Cys | missense_variant | Exon 20 of 66 | 5 | ENSP00000480802.2 | |||
LAMA2 | ENST00000617695.5 | c.2755C>T | p.Arg919Cys | missense_variant | Exon 20 of 64 | 5 | ENSP00000481744.2 |
Frequencies
GnomAD3 genomes AF: 0.000959 AC: 146AN: 152196Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000298 AC: 75AN: 251358Hom.: 1 AF XY: 0.000221 AC XY: 30AN XY: 135850
GnomAD4 exome AF: 0.000152 AC: 222AN: 1460650Hom.: 4 Cov.: 30 AF XY: 0.000125 AC XY: 91AN XY: 726726
GnomAD4 genome AF: 0.000965 AC: 147AN: 152314Hom.: 1 Cov.: 33 AF XY: 0.000966 AC XY: 72AN XY: 74496
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
- -
- -
- -
LAMA2-related muscular dystrophy Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at