rs749236548
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_033087.4(ALG2):c.304C>T(p.Leu102=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000972 in 1,543,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L102L) has been classified as Likely benign.
Frequency
Consequence
NM_033087.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG2 | NM_033087.4 | c.304C>T | p.Leu102= | synonymous_variant | 1/2 | ENST00000476832.2 | |
ALG2 | NR_024532.2 | n.352C>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG2 | ENST00000476832.2 | c.304C>T | p.Leu102= | synonymous_variant | 1/2 | 1 | NM_033087.4 | P1 | |
ALG2 | ENST00000238477.5 | c.304C>T | p.Leu102= | synonymous_variant, NMD_transcript_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152116Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000435 AC: 6AN: 137802Hom.: 0 AF XY: 0.0000533 AC XY: 4AN XY: 75070
GnomAD4 exome AF: 0.00000934 AC: 13AN: 1391752Hom.: 0 Cov.: 32 AF XY: 0.00000728 AC XY: 5AN XY: 686610
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74448
ClinVar
Submissions by phenotype
ALG2-congenital disorder of glycosylation;C4015597:Congenital myasthenic syndrome 14 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at