14-73858867-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001371330.1(PTGR2):c.-491T>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,459,020 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 (★).
Frequency
Consequence
NM_001371330.1 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTGR2 | ENST00000555661.6 | c.5T>C | p.Ile2Thr | missense_variant | Exon 2 of 10 | 1 | NM_001146154.2 | ENSP00000452280.1 | ||
ENSG00000258653 | ENST00000556551.2 | n.5T>C | non_coding_transcript_exon_variant | Exon 2 of 22 | 2 | ENSP00000451484.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251268Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135824
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459020Hom.: 0 Cov.: 28 AF XY: 0.00000276 AC XY: 2AN XY: 725858
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5T>C (p.I2T) alteration is located in exon 2 (coding exon 1) of the PTGR2 gene. This alteration results from a T to C substitution at nucleotide position 5, causing the isoleucine (I) at amino acid position 2 to be replaced by a threonine (T). 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