19-49851345-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000391842.6(PTOV1):c.17G>A(p.Arg6His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 138,278 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R6C) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000391842.6 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTOV1 | NM_001394010.1 | c.17G>A | p.Arg6His | missense_variant | 1/12 | ENST00000391842.6 | NP_001380939.1 | |
PTOV1-AS1 | NR_040037.1 | n.109+223C>T | intron_variant, non_coding_transcript_variant | |||||
PTOV1 | NR_130963.2 | n.251+390G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTOV1 | ENST00000391842.6 | c.17G>A | p.Arg6His | missense_variant | 1/12 | 5 | NM_001394010.1 | ENSP00000375717 | P1 | |
PTOV1-AS1 | ENST00000596521.1 | n.109+223C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000434 AC: 6AN: 138278Hom.: 0 Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 939462Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 440630
GnomAD4 genome AF: 0.0000434 AC: 6AN: 138278Hom.: 0 Cov.: 31 AF XY: 0.0000603 AC XY: 4AN XY: 66354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | The c.17G>A (p.R6H) alteration is located in exon 1 (coding exon 1) of the PTOV1 gene. This alteration results from a G to A substitution at nucleotide position 17, causing the arginine (R) at amino acid position 6 to be replaced by a histidine (H). 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