1-78493185-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000959.4(PTGFR):āc.442A>Gā(p.Thr148Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,614,112 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 (ā ).
Frequency
Consequence
NM_000959.4 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 |
---|---|---|---|---|---|---|---|---|
PTGFR | NM_000959.4 | c.442A>G | p.Thr148Ala | missense_variant | 2/3 | ENST00000370757.8 | NP_000950.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTGFR | ENST00000370757.8 | c.442A>G | p.Thr148Ala | missense_variant | 2/3 | 1 | NM_000959.4 | ENSP00000359793 | P1 | |
PTGFR | ENST00000370758.5 | c.442A>G | p.Thr148Ala | missense_variant | 3/4 | 1 | ENSP00000359794 | P1 | ||
PTGFR | ENST00000370756.3 | c.442A>G | p.Thr148Ala | missense_variant | 2/4 | 1 | ENSP00000359792 | |||
PTGFR | ENST00000497923.5 | c.442A>G | p.Thr148Ala | missense_variant, NMD_transcript_variant | 2/5 | 3 | ENSP00000432599 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251444Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135888
GnomAD4 exome AF: 0.0000451 AC: 66AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727246
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2021 | The c.442A>G (p.T148A) alteration is located in exon 2 (coding exon 1) of the PTGFR gene. This alteration results from a A to G substitution at nucleotide position 442, causing the threonine (T) at amino acid position 148 to be replaced by an alanine (A). 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