19-49851350-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000391842.6(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
ENST00000391842.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTOV1 | NM_001394010.1 | c.22C>T | p.Pro8Ser | missense_variant | 1/12 | ENST00000391842.6 | |
PTOV1-AS1 | NR_040037.1 | n.109+218G>A | intron_variant, non_coding_transcript_variant | ||||
PTOV1 | NR_130963.2 | n.251+395C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTOV1 | ENST00000391842.6 | c.22C>T | p.Pro8Ser | missense_variant | 1/12 | 5 | NM_001394010.1 | P1 | |
PTOV1-AS1 | ENST00000596521.1 | n.109+218G>A | intron_variant, non_coding_transcript_variant | 1 |
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
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | 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