rs748947069
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_033087.4(ALG2):c.729A>T(p.Ala243Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000882 in 1,461,894 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 (★).
Frequency
Consequence
NM_033087.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALG2 | NM_033087.4 | c.729A>T | p.Ala243Ala | synonymous_variant | Exon 2 of 2 | ENST00000476832.2 | NP_149078.1 | |
ALG2 | XM_047423996.1 | c.450A>T | p.Ala150Ala | synonymous_variant | Exon 2 of 2 | XP_047279952.1 | ||
ALG2 | NR_024532.2 | n.936A>T | non_coding_transcript_exon_variant | Exon 3 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALG2 | ENST00000476832.2 | c.729A>T | p.Ala243Ala | synonymous_variant | Exon 2 of 2 | 1 | NM_033087.4 | ENSP00000417764.1 | ||
ALG2 | ENST00000319033.7 | c.450A>T | p.Ala150Ala | synonymous_variant | Exon 2 of 2 | 1 | ENSP00000326609.6 | |||
ALG2 | ENST00000238477.5 | n.*471A>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | ENSP00000432675.2 | ||||
ALG2 | ENST00000238477.5 | n.*471A>T | 3_prime_UTR_variant | Exon 3 of 3 | 2 | ENSP00000432675.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251488Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135916
GnomAD4 exome AF: 0.0000882 AC: 129AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000770 AC XY: 56AN XY: 727248
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
ALG2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
ALG2-congenital disorder of glycosylation;C4015597:Congenital myasthenic syndrome 14 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at