chr14-52274956-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000953.3(PTGDR):c.1072A>T(p.Ser358Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000714 in 1,401,466 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_000953.3 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 | UniProt |
---|---|---|---|---|---|---|---|
PTGDR | NM_000953.3 | c.1072A>T | p.Ser358Cys | missense_variant | 2/2 | ENST00000306051.3 | |
PTGDR | XM_005267891.5 | c.1072A>T | p.Ser358Cys | missense_variant | 2/3 | ||
PTGDR | NM_001281469.2 | c.*272A>T | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGDR | ENST00000306051.3 | c.1072A>T | p.Ser358Cys | missense_variant | 2/2 | 1 | NM_000953.3 | P1 | |
PTGDR | ENST00000553372.1 | c.*272A>T | 3_prime_UTR_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 7.14e-7 AC: 1AN: 1401466Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 699250
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2023 | The c.1072A>T (p.S358C) alteration is located in exon 2 (coding exon 2) of the PTGDR gene. This alteration results from a A to T substitution at nucleotide position 1072, causing the serine (S) at amino acid position 358 to be replaced by a cysteine (C). 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