chr9-99221728-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_033087.4(ALG2):c.167C>T(p.Pro56Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000342 in 1,598,192 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P56P) has been classified as Uncertain significance.
Frequency
Consequence
NM_033087.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG2 | NM_033087.4 | c.167C>T | p.Pro56Leu | missense_variant | 1/2 | ENST00000476832.2 | |
ALG2 | NR_024532.2 | n.215C>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG2 | ENST00000476832.2 | c.167C>T | p.Pro56Leu | missense_variant | 1/2 | 1 | NM_033087.4 | P1 | |
ALG2 | ENST00000238477.5 | c.167C>T | p.Pro56Leu | missense_variant, NMD_transcript_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000585 AC: 89AN: 152236Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000930 AC: 206AN: 221450Hom.: 0 AF XY: 0.000826 AC XY: 102AN XY: 123484
GnomAD4 exome AF: 0.000315 AC: 456AN: 1445838Hom.: 3 Cov.: 32 AF XY: 0.000340 AC XY: 245AN XY: 719758
GnomAD4 genome AF: 0.000597 AC: 91AN: 152354Hom.: 1 Cov.: 33 AF XY: 0.000671 AC XY: 50AN XY: 74508
ClinVar
Submissions by phenotype
ALG2-congenital disorder of glycosylation;C4015597:Congenital myasthenic syndrome 14 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 10, 2022 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jun 22, 2023 | BS1 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 15, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at