rs104894274
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_000317.3(PTS):c.46C>T(p.Arg16Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000296 in 1,586,340 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000317.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000198 AC: 4AN: 202108Hom.: 0 AF XY: 0.0000183 AC XY: 2AN XY: 109100
GnomAD4 exome AF: 0.0000314 AC: 45AN: 1434196Hom.: 0 Cov.: 31 AF XY: 0.0000281 AC XY: 20AN XY: 710510
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74316
ClinVar
Submissions by phenotype
Hyperphenylalaninemia, bh4-deficient, a, due to partial pts deficiency Pathogenic:1
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6-Pyruvoyl-tetrahydrobiopterin synthase deficiency Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at