14-52268642-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000953.3(PTGDR):c.828G>A(p.Met276Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000209 in 1,432,246 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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.828G>A | p.Met276Ile | missense_variant | 1/2 | ENST00000306051.3 | |
PTGDR | NM_001281469.2 | c.828G>A | p.Met276Ile | missense_variant | 1/3 | ||
PTGDR | XM_005267891.5 | c.828G>A | p.Met276Ile | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGDR | ENST00000306051.3 | c.828G>A | p.Met276Ile | missense_variant | 1/2 | 1 | NM_000953.3 | P1 | |
PTGDR | ENST00000553372.1 | c.828G>A | p.Met276Ile | missense_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000209 AC: 3AN: 1432246Hom.: 0 Cov.: 31 AF XY: 0.00000282 AC XY: 2AN XY: 709154
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | PTGDR: PM2, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.