12-102855316-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000277.3(PAH):c.526C>A(p.Arg176Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000277.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAH | NM_000277.3 | c.526C>A | p.Arg176Arg | synonymous_variant | Exon 6 of 13 | ENST00000553106.6 | NP_000268.1 | |
PAH | NM_001354304.2 | c.526C>A | p.Arg176Arg | synonymous_variant | Exon 7 of 14 | NP_001341233.1 | ||
PAH | XM_017019370.2 | c.526C>A | p.Arg176Arg | synonymous_variant | Exon 6 of 7 | XP_016874859.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAH | ENST00000553106.6 | c.526C>A | p.Arg176Arg | synonymous_variant | Exon 6 of 13 | 1 | NM_000277.3 | ENSP00000448059.1 | ||
PAH | ENST00000549111.5 | n.622C>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 1 | |||||
PAH | ENST00000307000.7 | c.511C>A | p.Arg171Arg | synonymous_variant | Exon 7 of 14 | 5 | ENSP00000303500.2 | |||
PAH | ENST00000551988.5 | n.547C>A | non_coding_transcript_exon_variant | Exon 5 of 5 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461816Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727218
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Phenylketonuria Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.