rs754062242
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_Strong
The ENST00000352480.10(ASS1):āc.839G>Cā(p.Gly280Ala) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,428 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 14/23 in silico tools predict a damaging outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G280V) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000352480.10 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASS1 | NM_054012.4 | c.839G>C | p.Gly280Ala | missense_variant, splice_region_variant | 12/15 | ENST00000352480.10 | NP_446464.1 | |
ASS1 | NM_000050.4 | c.839G>C | p.Gly280Ala | missense_variant, splice_region_variant | 13/16 | NP_000041.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ASS1 | ENST00000352480.10 | c.839G>C | p.Gly280Ala | missense_variant, splice_region_variant | 12/15 | 1 | NM_054012.4 | ENSP00000253004 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151732Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251418Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135900
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461696Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727166
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151732Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74052
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at