rs774875437
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_000426.4(LAMA2):āc.4786A>Gā(p.Ile1596Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,461,832 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000426.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.4786A>G | p.Ile1596Val | missense_variant | 33/65 | ENST00000421865.3 | |
LAMA2 | NM_001079823.2 | c.4786A>G | p.Ile1596Val | missense_variant | 33/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.4786A>G | p.Ile1596Val | missense_variant | 33/65 | 5 | NM_000426.4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251002Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135626
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461832Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727220
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.4786A>G (p.I1596V) alteration is located in exon 33 (coding exon 33) of the LAMA2 gene. This alteration results from a A to G substitution at nucleotide position 4786, causing the isoleucine (I) at amino acid position 1596 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
LAMA2-related muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at