chr19-40394517-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_181882.3(PRX):c.3835G>A(p.Val1279Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000483 in 1,448,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1279L) has been classified as Uncertain significance.
Frequency
Consequence
NM_181882.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRX | NM_181882.3 | c.3835G>A | p.Val1279Met | missense_variant | 7/7 | ENST00000324001.8 | |
PRX | NM_001411127.1 | c.4120G>A | p.Val1374Met | missense_variant | 7/7 | ||
PRX | XM_017027047.2 | c.3733G>A | p.Val1245Met | missense_variant | 4/4 | ||
PRX | NM_020956.2 | c.*4040G>A | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRX | ENST00000324001.8 | c.3835G>A | p.Val1279Met | missense_variant | 7/7 | 1 | NM_181882.3 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000449 AC: 1AN: 222790Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 121676
GnomAD4 exome AF: 0.00000483 AC: 7AN: 1448158Hom.: 0 Cov.: 33 AF XY: 0.00000417 AC XY: 3AN XY: 719816
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at