rs1336047164
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_005787.6(ALG3):c.194C>T(p.Ala65Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000241 in 1,246,132 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_005787.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALG3 | NM_005787.6 | c.194C>T | p.Ala65Val | missense_variant, splice_region_variant | Exon 1 of 9 | ENST00000397676.8 | NP_005778.1 | |
ALG3 | NM_001006941.2 | c.52+479C>T | intron_variant | Intron 1 of 8 | NP_001006942.1 | |||
ALG3 | NR_024533.1 | n.225C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 1 of 8 | ||||
ALG3 | NR_024534.1 | n.190+35C>T | intron_variant | Intron 1 of 8 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000676 AC: 1AN: 147854Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1098278Hom.: 0 Cov.: 35 AF XY: 0.00000184 AC XY: 1AN XY: 542808
GnomAD4 genome AF: 0.00000676 AC: 1AN: 147854Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 72058
ClinVar
Submissions by phenotype
not provided Uncertain:2
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on splicing; In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at