19-49851350-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_017432.5(PTOV1):c.22C>T(p.Pro8Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000513 in 1,098,286 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017432.5 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 |
---|---|---|---|---|---|---|---|---|
PTOV1 | NM_001305105.2 | c.22C>T | p.Pro8Ser | missense_variant | Exon 1 of 13 | NP_001292034.1 | ||
PTOV1 | NM_001394010.1 | c.22C>T | p.Pro8Ser | missense_variant | Exon 1 of 12 | NP_001380939.1 | ||
PTOV1 | NM_017432.5 | c.22C>T | p.Pro8Ser | missense_variant | Exon 1 of 13 | NP_059128.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00256 AC: 380AN: 148246Hom.: 1 Cov.: 31
GnomAD4 exome AF: 0.000192 AC: 182AN: 949932Hom.: 3 Cov.: 32 AF XY: 0.000168 AC XY: 75AN XY: 446146
GnomAD4 genome AF: 0.00257 AC: 381AN: 148354Hom.: 1 Cov.: 31 AF XY: 0.00250 AC XY: 181AN XY: 72394
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.22C>T (p.P8S) alteration is located in exon 1 (coding exon 1) of the PTOV1 gene. This alteration results from a C to T substitution at nucleotide position 22, causing the proline (P) at amino acid position 8 to be replaced by a serine (S). 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