13-36995455-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_013338.5(ALG5):c.208G>A(p.Val70Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,612,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_013338.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG5 | NM_013338.5 | c.208G>A | p.Val70Ile | missense_variant | 2/10 | ENST00000239891.4 | |
ALG5 | NM_001142364.1 | c.208G>A | p.Val70Ile | missense_variant | 2/9 | ||
ALG5 | XM_047430283.1 | c.66G>A | p.Ser22= | synonymous_variant | 1/8 | ||
ALG5 | XR_007063678.1 | n.248G>A | non_coding_transcript_exon_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG5 | ENST00000239891.4 | c.208G>A | p.Val70Ile | missense_variant | 2/10 | 1 | NM_013338.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 30AN: 250038Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135076
GnomAD4 exome AF: 0.0000760 AC: 111AN: 1460514Hom.: 0 Cov.: 31 AF XY: 0.0000785 AC XY: 57AN XY: 726474
GnomAD4 genome AF: 0.000361 AC: 55AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74474
ClinVar
Submissions by phenotype
ALG5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 28, 2023 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at