rs148451013
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000426.4(LAMA2):āc.5909G>Cā(p.Cys1970Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000532 in 1,613,834 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_000426.4 missense
Scores
Clinical Significance
Conservation
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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.5909G>C | p.Cys1970Ser | missense_variant | Exon 41 of 65 | 5 | NM_000426.4 | ENSP00000400365.2 | ||
LAMA2 | ENST00000618192.5 | c.6173G>C | p.Cys2058Ser | missense_variant | Exon 42 of 66 | 5 | ENSP00000480802.2 | |||
LAMA2 | ENST00000617695.5 | c.5909G>C | p.Cys1970Ser | missense_variant | Exon 41 of 64 | 5 | ENSP00000481744.2 |
Frequencies
GnomAD3 genomes AF: 0.00283 AC: 431AN: 152170Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000784 AC: 197AN: 251268Hom.: 3 AF XY: 0.000493 AC XY: 67AN XY: 135816
GnomAD4 exome AF: 0.000293 AC: 428AN: 1461546Hom.: 3 Cov.: 30 AF XY: 0.000250 AC XY: 182AN XY: 727104
GnomAD4 genome AF: 0.00283 AC: 431AN: 152288Hom.: 2 Cov.: 32 AF XY: 0.00267 AC XY: 199AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:4
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
LAMA2-related muscular dystrophy Benign:1
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LAMA2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at