chr20-62309398-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005560.6(LAMA5):c.11026G>A(p.Ala3676Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000479 in 1,587,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005560.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA5 | NM_005560.6 | c.11026G>A | p.Ala3676Thr | missense_variant | 80/80 | ENST00000252999.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA5 | ENST00000252999.7 | c.11026G>A | p.Ala3676Thr | missense_variant | 80/80 | 1 | NM_005560.6 | P1 | |
LAMA5 | ENST00000370691.6 | n.2821G>A | non_coding_transcript_exon_variant | 17/17 | 1 | ||||
LAMA5 | ENST00000495695.1 | n.527G>A | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 151962Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000429 AC: 9AN: 209692Hom.: 0 AF XY: 0.0000432 AC XY: 5AN XY: 115850
GnomAD4 exome AF: 0.0000495 AC: 71AN: 1435776Hom.: 0 Cov.: 32 AF XY: 0.0000491 AC XY: 35AN XY: 713468
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 151962Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74212
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2023 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at