6-129313068-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000426.4(LAMA2):āc.3382A>Gā(p.Ser1128Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,612,012 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. S1128S) has been classified as Likely benign.
Frequency
Consequence
NM_000426.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.3382A>G | p.Ser1128Gly | missense_variant | 23/65 | ENST00000421865.3 | |
LAMA2 | NM_001079823.2 | c.3382A>G | p.Ser1128Gly | missense_variant | 23/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.3382A>G | p.Ser1128Gly | missense_variant | 23/65 | 5 | NM_000426.4 | ||
LAMA2 | ENST00000618192.5 | c.3646A>G | p.Ser1216Gly | missense_variant | 24/66 | 5 | P1 | ||
LAMA2 | ENST00000617695.5 | c.3382A>G | p.Ser1128Gly | missense_variant | 23/64 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000291 AC: 73AN: 250972Hom.: 0 AF XY: 0.000413 AC XY: 56AN XY: 135628
GnomAD4 exome AF: 0.000133 AC: 194AN: 1459656Hom.: 2 Cov.: 31 AF XY: 0.000207 AC XY: 150AN XY: 725738
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74508
ClinVar
Submissions by phenotype
LAMA2-related muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at