rs141235562
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000426.4(LAMA2):c.5405G>A(p.Arg1802His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. R1802L) has been classified as Uncertain significance.
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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.5405G>A | p.Arg1802His | missense_variant | 37/65 | ENST00000421865.3 | |
LAMA2 | NM_001079823.2 | c.5405G>A | p.Arg1802His | missense_variant | 37/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.5405G>A | p.Arg1802His | missense_variant | 37/65 | 5 | NM_000426.4 | ||
LAMA2 | ENST00000618192.5 | c.5669G>A | p.Arg1890His | missense_variant | 38/66 | 5 | P1 | ||
LAMA2 | ENST00000617695.5 | c.5405G>A | p.Arg1802His | missense_variant | 37/64 | 5 | |||
LAMA2 | ENST00000687590.1 | n.1825G>A | non_coding_transcript_exon_variant | 5/5 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251262Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135798
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461736Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727172
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74326
ClinVar
Submissions by phenotype
LAMA2-related muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at