chr5-149365573-A-G

Variant names:

• chr5-149365573-A-G
• rs2242376
• ENST00000507621.1:n.2505A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507621.1(PCYOX1L):​n.2505A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 266,218 control chromosomes in the GnomAD database, including 38,156 homozygotes. 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: 𝑓 0.55 (24436 hom., cov: 32)
  • Exomes 𝑓: 0.47 (13720 hom.)
• Consequence: PCYOX1L ENST00000507621.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84233 AN: 151912 Hom.: 24391 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.538

GnomAD4 exome AF: 0.474 AC: 54162 AN: 114188 Hom.: 13720 Cov.: 0 AF XY: 0.460 AC XY: 27627 AN XY: 60094

African (AFR) AF: 0.718 AC: 2850 AN: 3972

American (AMR) AF: 0.413 AC: 2079 AN: 5028

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1481 AN: 3138

East Asian (EAS) AF: 0.326 AC: 1737 AN: 5330

South Asian (SAS) AF: 0.340 AC: 5507 AN: 16204

European-Finnish (FIN) AF: 0.524 AC: 2842 AN: 5420

Middle Eastern (MID) AF: 0.502 AC: 255 AN: 508

European-Non Finnish (NFE) AF: 0.502 AC: 34219 AN: 68206

Other (OTH) AF: 0.500 AC: 3192 AN: 6382

GnomAD4 genome AF: 0.555 AC: 84330 AN: 152030 Hom.: 24436 Cov.: 32 AF XY: 0.547 AC XY: 40677 AN XY: 74312

African (AFR) AF: 0.725 AC: 30057 AN: 41476

American (AMR) AF: 0.456 AC: 6960 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1693 AN: 3472

East Asian (EAS) AF: 0.324 AC: 1672 AN: 5166

South Asian (SAS) AF: 0.341 AC: 1644 AN: 4816

European-Finnish (FIN) AF: 0.561 AC: 5920 AN: 10550

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.511 AC: 34753 AN: 67970

Other (OTH) AF: 0.536 AC: 1130 AN: 2108

Alfa AF: 0.544 Hom.: 3789

Bravo AF: 0.556

Asia WGS AF: 0.385 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.64
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2242376; hg19: chr5-148745136;