rs758353539
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001367806.1(PYGO1):c.328G>T(p.Val110Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,774 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. 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. V110I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001367806.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PYGO1 | NM_001367806.1 | c.328G>T | p.Val110Phe | missense_variant | Exon 3 of 3 | ENST00000563719.4 | NP_001354735.1 | |
PYGO1 | NM_001330326.2 | c.328G>T | p.Val110Phe | missense_variant | Exon 3 of 4 | NP_001317255.1 | ||
PYGO1 | NM_015617.3 | c.328G>T | p.Val110Phe | missense_variant | Exon 3 of 3 | NP_056432.1 | ||
PYGO1 | XM_047432381.1 | c.13G>T | p.Val5Phe | missense_variant | Exon 3 of 3 | XP_047288337.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PYGO1 | ENST00000563719.4 | c.328G>T | p.Val110Phe | missense_variant | Exon 3 of 3 | 5 | NM_001367806.1 | ENSP00000457777.1 | ||
PYGO1 | ENST00000302000.10 | c.328G>T | p.Val110Phe | missense_variant | Exon 3 of 3 | 1 | ENSP00000302327.6 | |||
PYGO1 | ENST00000645724.1 | c.328G>T | p.Val110Phe | missense_variant | Exon 3 of 4 | ENSP00000496139.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251258Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135778
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461774Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727192
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at