5-149365573-A-T

Variant names:

• chr5-149365573-A-T
• rs2242376
• NM_024028.4:c.471-369A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_024028.4(PCYOX1L):​c.471-369A>T variant causes a intron 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 NM_024028.4 intron
• 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: 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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024028.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCYOX1L	NM_024028.4	MANE Select	c.471-369A>T		intron	N/A	NP_076933.3
	PCYOX1L	NM_001301054.2		c.420-369A>T		intron	N/A	NP_001287983.1
	PCYOX1L	NM_001301057.2		c.420-546A>T		intron	N/A	NP_001287986.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCYOX1L	ENST00000274569.9	TSL:2 MANE Select	c.471-369A>T		intron	N/A	ENSP00000274569.4	Q8NBM8-1
	PCYOX1L	ENST00000507621.1	TSL:1	n.2505A>T		non_coding_transcript_exon	Exon 1 of 3
	PCYOX1L	ENST00000505669.5	TSL:1	n.*238-546A>T		intron	N/A	ENSP00000427166.1	Q8NBM8-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 114652 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 60328

African (AFR) AF: 0.00 AC: 0 AN: 3988

American (AMR) AF: 0.00 AC: 0 AN: 5048

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3150

East Asian (EAS) AF: 0.00 AC: 0 AN: 5348

South Asian (SAS) AF: 0.00 AC: 0 AN: 16256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5454

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 508

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68496

Other (OTH) AF: 0.00 AC: 0 AN: 6404

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism

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;