19-49851444-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000391842.6(PTOV1):c.116C>T(p.Ala39Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000123 in 1,220,022 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTOV1 | NM_001394010.1 | c.116C>T | p.Ala39Val | missense_variant | 1/12 | ENST00000391842.6 | NP_001380939.1 | |
PTOV1-AS1 | NR_040037.1 | n.109+124G>A | intron_variant, non_coding_transcript_variant | |||||
PTOV1 | NR_130963.2 | n.251+489C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTOV1 | ENST00000391842.6 | c.116C>T | p.Ala39Val | missense_variant | 1/12 | 5 | NM_001394010.1 | ENSP00000375717 | P1 | |
PTOV1-AS1 | ENST00000596521.1 | n.109+124G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000331 AC: 5AN: 151188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00225 AC: 1AN: 444Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 264
GnomAD4 exome AF: 0.00000936 AC: 10AN: 1068834Hom.: 0 Cov.: 31 AF XY: 0.0000139 AC XY: 7AN XY: 505192
GnomAD4 genome AF: 0.0000331 AC: 5AN: 151188Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73822
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.116C>T (p.A39V) 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 116, causing the alanine (A) at amino acid position 39 to be replaced by a valine (V). 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