NM_001367806.1:c.328G>A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001367806.1(PYGO1):c.328G>A(p.Val110Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001367806.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PYGO1 | NM_001367806.1 | c.328G>A | p.Val110Ile | missense_variant | Exon 3 of 3 | ENST00000563719.4 | NP_001354735.1 | |
PYGO1 | NM_001330326.2 | c.328G>A | p.Val110Ile | missense_variant | Exon 3 of 4 | NP_001317255.1 | ||
PYGO1 | NM_015617.3 | c.328G>A | p.Val110Ile | missense_variant | Exon 3 of 3 | NP_056432.1 | ||
PYGO1 | XM_047432381.1 | c.13G>A | p.Val5Ile | 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>A | p.Val110Ile | missense_variant | Exon 3 of 3 | 5 | NM_001367806.1 | ENSP00000457777.1 | ||
PYGO1 | ENST00000302000.10 | c.328G>A | p.Val110Ile | missense_variant | Exon 3 of 3 | 1 | ENSP00000302327.6 | |||
PYGO1 | ENST00000645724.1 | c.328G>A | p.Val110Ile | missense_variant | Exon 3 of 4 | ENSP00000496139.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151968Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251258Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135778
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461774Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727192
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151968Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74212
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.328G>A (p.V110I) alteration is located in exon 3 (coding exon 3) of the PYGO1 gene. This alteration results from a G to A substitution at nucleotide position 328, causing the valine (V) at amino acid position 110 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at