chr5-149358088-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024028.4(PCYOX1L):c.20T>A(p.Leu7Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000778 in 1,284,640 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 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 Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCYOX1L | NM_024028.4 | c.20T>A | p.Leu7Gln | missense_variant | 1/6 | ENST00000274569.9 | |
PCYOX1L | NM_001301054.2 | c.-48T>A | 5_prime_UTR_variant | 1/6 | |||
PCYOX1L | NM_001301057.2 | c.-48T>A | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCYOX1L | ENST00000274569.9 | c.20T>A | p.Leu7Gln | missense_variant | 1/6 | 2 | NM_024028.4 | P1 | |
PCYOX1L | ENST00000505669.5 | c.20T>A | p.Leu7Gln | missense_variant, NMD_transcript_variant | 1/6 | 1 | |||
PCYOX1L | ENST00000511945.5 | c.20T>A | p.Leu7Gln | missense_variant, NMD_transcript_variant | 1/6 | 1 | |||
PCYOX1L | ENST00000510990.6 | c.20T>A | p.Leu7Gln | missense_variant, NMD_transcript_variant | 1/5 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 7.78e-7 AC: 1AN: 1284640Hom.: 0 Cov.: 31 AF XY: 0.00000158 AC XY: 1AN XY: 631976
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2022 | The c.20T>A (p.L7Q) alteration is located in exon 1 (coding exon 1) of the PCYOX1L gene. This alteration results from a T to A substitution at nucleotide position 20, causing the leucine (L) at amino acid position 7 to be replaced by a glutamine (Q). 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
Publications
No publications associated with this variant yet.