5-149368017-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024028.4(PCYOX1L):c.848C>T(p.Ala283Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,545,018 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_024028.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCYOX1L | NM_024028.4 | c.848C>T | p.Ala283Val | missense_variant | 6/6 | ENST00000274569.9 | |
PCYOX1L | NM_001301054.2 | c.797C>T | p.Ala266Val | missense_variant | 6/6 | ||
PCYOX1L | NM_001301057.2 | c.620C>T | p.Ala207Val | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCYOX1L | ENST00000274569.9 | c.848C>T | p.Ala283Val | missense_variant | 6/6 | 2 | NM_024028.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000312 AC: 6AN: 192206Hom.: 0 AF XY: 0.0000197 AC XY: 2AN XY: 101350
GnomAD4 exome AF: 0.00000933 AC: 13AN: 1392728Hom.: 0 Cov.: 31 AF XY: 0.00000874 AC XY: 6AN XY: 686432
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 26, 2022 | The c.848C>T (p.A283V) alteration is located in exon 6 (coding exon 6) of the PCYOX1L gene. This alteration results from a C to T substitution at nucleotide position 848, causing the alanine (A) at amino acid position 283 to be replaced by a valine (V). 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