chr3-184245333-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_005787.6(ALG3):c.470T>A(p.Met157Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,758 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M157V) has been classified as Uncertain significance.
Frequency
Consequence
NM_005787.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG3 | NM_005787.6 | c.470T>A | p.Met157Lys | missense_variant | 4/9 | ENST00000397676.8 | |
ALG3 | NM_001006941.2 | c.326T>A | p.Met109Lys | missense_variant | 4/9 | ||
ALG3 | NR_024533.1 | n.401T>A | non_coding_transcript_exon_variant | 3/8 | |||
ALG3 | NR_024534.1 | n.464T>A | non_coding_transcript_exon_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG3 | ENST00000397676.8 | c.470T>A | p.Met157Lys | missense_variant | 4/9 | 1 | NM_005787.6 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460758Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726590
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
ALG3-congenital disorder of glycosylation Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2007 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at