chr1-116945057-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020440.4(PTGFRN):c.797C>T(p.Ala266Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,613,276 control chromosomes in the GnomAD database, including 1 homozygotes. 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_020440.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGFRN | NM_020440.4 | c.797C>T | p.Ala266Val | missense_variant | 3/9 | ENST00000393203.3 | |
PTGFRN | XM_017001874.2 | c.815C>T | p.Ala272Val | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGFRN | ENST00000393203.3 | c.797C>T | p.Ala266Val | missense_variant | 3/9 | 1 | NM_020440.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000144 AC: 36AN: 249310Hom.: 1 AF XY: 0.000133 AC XY: 18AN XY: 135136
GnomAD4 exome AF: 0.000114 AC: 167AN: 1461082Hom.: 1 Cov.: 33 AF XY: 0.000105 AC XY: 76AN XY: 726874
GnomAD4 genome AF: 0.000105 AC: 16AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.797C>T (p.A266V) alteration is located in exon 3 (coding exon 3) of the PTGFRN gene. This alteration results from a C to T substitution at nucleotide position 797, causing the alanine (A) at amino acid position 266 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