5-149358152-A-G

Variant names:

• chr5-149358152-A-G
• rs1198809395
• NM_024028.4:c.84A>G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001301054.2(PCYOX1L):​c.17A>G​(p.Lys6Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000767 in 1,303,180 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. K6I) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.7e-7 (0 hom.)
• Consequence: PCYOX1L NM_001301054.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 0 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]

GRPEL2-AS1 (HGNC:48999): (GRPEL2 antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001301054.2. 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.84A>G	p.Lys28Lys	synonymous	Exon 1 of 6	NP_076933.3
	PCYOX1L	NM_001301054.2		c.17A>G	p.Lys6Arg	missense	Exon 1 of 6	NP_001287983.1
	PCYOX1L	NM_001301057.2		c.17A>G	p.Lys6Arg	missense	Exon 1 of 6	NP_001287986.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCYOX1L	ENST00000274569.9	TSL:2 MANE Select	c.84A>G	p.Lys28Lys	synonymous	Exon 1 of 6	ENSP00000274569.4	Q8NBM8-1
	PCYOX1L	ENST00000505669.5	TSL:1	n.84A>G		non_coding_transcript_exon	Exon 1 of 6	ENSP00000427166.1	Q8NBM8-2
	PCYOX1L	ENST00000511945.5	TSL:1	n.84A>G		non_coding_transcript_exon	Exon 1 of 6	ENSP00000426091.1	Q8NBM8-2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.67e-7 AC: 1 AN: 1303180 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 641918

African (AFR) AF: 0.00 AC: 0 AN: 26520

American (AMR) AF: 0.00 AC: 0 AN: 24984

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22890

East Asian (EAS) AF: 0.00 AC: 0 AN: 27910

South Asian (SAS) AF: 0.00 AC: 0 AN: 70460

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33988

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3818

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1038830

Other (OTH) AF: 0.0000186 AC: 1 AN: 53780

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	17
DANN	Benign	0.77
PhyloP100		1.2
PromoterAI		0.15	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.22		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.22		Position offset: 20

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

Other links and lift over

dbSNP: rs1198809395; hg19: chr5-148737715;