chr13-36965725-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_013338.5(ALG5):c.623G>A(p.Arg208His) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000311 in 1,606,566 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_013338.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG5 | NM_013338.5 | c.623G>A | p.Arg208His | missense_variant, splice_region_variant | 8/10 | ENST00000239891.4 | |
ALG5 | NM_001142364.1 | c.533G>A | p.Arg178His | missense_variant, splice_region_variant | 7/9 | ||
ALG5 | XM_047430283.1 | c.434G>A | p.Arg145His | missense_variant, splice_region_variant | 6/8 | ||
ALG5 | XR_007063678.1 | n.799G>A | splice_region_variant, non_coding_transcript_exon_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG5 | ENST00000239891.4 | c.623G>A | p.Arg208His | missense_variant, splice_region_variant | 8/10 | 1 | NM_013338.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243508Hom.: 0 AF XY: 0.00000758 AC XY: 1AN XY: 131988
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1454446Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 2AN XY: 723740
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74308
ClinVar
Submissions by phenotype
Polycystic kidney disease 7 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at