rs531748488
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_033087.4(ALG2):c.216G>T(p.Gly72=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000454 in 1,565,558 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. G72G) has been classified as Likely benign.
Frequency
Consequence
NM_033087.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG2 | NM_033087.4 | c.216G>T | p.Gly72= | synonymous_variant | 1/2 | ENST00000476832.2 | |
ALG2 | NR_024532.2 | n.264G>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG2 | ENST00000476832.2 | c.216G>T | p.Gly72= | synonymous_variant | 1/2 | 1 | NM_033087.4 | P1 | |
ALG2 | ENST00000238477.5 | c.216G>T | p.Gly72= | synonymous_variant, NMD_transcript_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000296 AC: 45AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000658 AC: 11AN: 167072Hom.: 0 AF XY: 0.0000755 AC XY: 7AN XY: 92722
GnomAD4 exome AF: 0.0000184 AC: 26AN: 1413204Hom.: 0 Cov.: 32 AF XY: 0.0000200 AC XY: 14AN XY: 700184
GnomAD4 genome AF: 0.000295 AC: 45AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.000268 AC XY: 20AN XY: 74500
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 | Oct 23, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 06, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at