Genetic Variant PCYOX1L:n.2505A>T (chr5-149365573-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000507621.1(PCYOX1L):n.2505A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PCYOX1L
ENST00000507621.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.376

Publications

4 publications found

Variant links:

Genes affected

PCYOX1L (HGNC:28477): (prenylcysteine oxidase 1 like) Predicted to enable prenylcysteine oxidase activity. Predicted to be involved in prenylated protein catabolic process. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

PCYOX1L links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PCYOX1L	NM_024028.4 link	c.471-369A>T	intron_variant	Intron 3 of 5	ENST00000274569.9	NP_076933.3	Q8NBM8-1
PCYOX1L	NM_001301054.2 link	c.420-369A>T	intron_variant	Intron 3 of 5		NP_001287983.1	Q8NBM8
PCYOX1L	NM_001301057.2 link	c.420-546A>T	intron_variant	Intron 3 of 5		NP_001287986.1	Q8NBM8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCYOX1L	ENST00000274569.9 link	c.471-369A>T		intron_variant	Intron 3 of 5	2	NM_024028.4	ENSP00000274569.4		Q8NBM8-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

114652

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

60328

African (AFR)

AF:

0.00

AC:

AN:

3988

American (AMR)

AF:

0.00

AC:

AN:

5048

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3150

East Asian (EAS)

AF:

0.00

AC:

AN:

5348

South Asian (SAS)

AF:

0.00

AC:

AN:

16256

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5454

Middle Eastern (MID)

AF:

0.00

AC:

AN:

508

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68496

Other (OTH)

AF:

0.00

AC:

AN:

6404

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.3

(source)

DANN

Benign

0.70

PhyloP100

-0.38

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over