rs139843107
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BP6
The NM_000426.4(LAMA2):āc.2240G>Cā(p.Gly747Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G747S) 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.2240G>C | p.Gly747Ala | missense_variant | 16/65 | ENST00000421865.3 | |
LAMA2 | NM_001079823.2 | c.2240G>C | p.Gly747Ala | missense_variant | 16/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.2240G>C | p.Gly747Ala | missense_variant | 16/65 | 5 | NM_000426.4 | ||
LAMA2 | ENST00000618192.5 | c.2240G>C | p.Gly747Ala | missense_variant | 16/66 | 5 | P1 | ||
LAMA2 | ENST00000617695.5 | c.2240G>C | p.Gly747Ala | missense_variant | 16/64 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251062Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135672
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1460956Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726816
GnomAD4 genome AF: 0.000105 AC: 16AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74418
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 27, 2019 | - - |
Merosin deficient congenital muscular dystrophy;C4748327:Muscular dystrophy, limb-girdle, autosomal recessive 23 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 01, 2021 | - - |
LAMA2-related muscular dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at