chr5-149358085-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_024028.4(PCYOX1L):āc.17C>Gā(p.Pro6Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0005 in 1,433,036 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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. P6Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_024028.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCYOX1L | NM_024028.4 | c.17C>G | p.Pro6Arg | missense_variant | Exon 1 of 6 | ENST00000274569.9 | NP_076933.3 | |
PCYOX1L | NM_001301054.2 | c.-51C>G | 5_prime_UTR_variant | Exon 1 of 6 | NP_001287983.1 | |||
PCYOX1L | NM_001301057.2 | c.-51C>G | 5_prime_UTR_variant | Exon 1 of 6 | NP_001287986.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCYOX1L | ENST00000274569.9 | c.17C>G | p.Pro6Arg | missense_variant | Exon 1 of 6 | 2 | NM_024028.4 | ENSP00000274569.4 | ||
PCYOX1L | ENST00000505669.5 | n.17C>G | non_coding_transcript_exon_variant | Exon 1 of 6 | 1 | ENSP00000427166.1 | ||||
PCYOX1L | ENST00000511945.5 | n.17C>G | non_coding_transcript_exon_variant | Exon 1 of 6 | 1 | ENSP00000426091.1 | ||||
PCYOX1L | ENST00000510990.6 | n.17C>G | non_coding_transcript_exon_variant | Exon 1 of 5 | 4 | ENSP00000422063.2 |
Frequencies
GnomAD3 genomes AF: 0.000559 AC: 85AN: 152060Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00196 AC: 126AN: 64426Hom.: 0 AF XY: 0.00180 AC XY: 67AN XY: 37284
GnomAD4 exome AF: 0.000493 AC: 632AN: 1280864Hom.: 2 Cov.: 31 AF XY: 0.000480 AC XY: 302AN XY: 629750
GnomAD4 genome AF: 0.000559 AC: 85AN: 152172Hom.: 1 Cov.: 33 AF XY: 0.000618 AC XY: 46AN XY: 74410
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at