rs370971334
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_000426.4(LAMA2):c.4969G>A(p.Val1657Met) variant causes a missense change. The variant allele was found at a frequency of 0.000163 in 1,613,438 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. V1657V) has been classified as Likely benign.
Frequency
Consequence
NM_000426.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.4969G>A | p.Val1657Met | missense_variant | 35/65 | ENST00000421865.3 | |
LAMA2 | NM_001079823.2 | c.4969G>A | p.Val1657Met | missense_variant | 35/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.4969G>A | p.Val1657Met | missense_variant | 35/65 | 5 | NM_000426.4 | ||
LAMA2 | ENST00000618192.5 | c.5233G>A | p.Val1745Met | missense_variant | 36/66 | 5 | P1 | ||
LAMA2 | ENST00000617695.5 | c.4969G>A | p.Val1657Met | missense_variant | 35/64 | 5 | |||
LAMA2 | ENST00000687590.1 | n.1389G>A | non_coding_transcript_exon_variant | 3/5 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000156 AC: 39AN: 249888Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 134986
GnomAD4 exome AF: 0.000167 AC: 244AN: 1461224Hom.: 1 Cov.: 31 AF XY: 0.000166 AC XY: 121AN XY: 726906
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74354
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 18, 2014 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Apr 05, 2021 | - - |
LAMA2-related muscular dystrophy Benign:1Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpretted as Uncertain significance and reported on 02-08-2015 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 22, 2016 | - - |
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 | Oct 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at