8-51665854-T-C

Position:

• chr8-51665854-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144651.5(PXDNL):​c.165-11094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,186 control chromosomes in the GnomAD database, including 54,208 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 0.84 (54208 hom., cov: 32)
• Consequence: PXDNL NM_144651.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

PXDNL (HGNC:26359): (peroxidasin like) Predicted to enable heme binding activity and peroxidase activity. Predicted to be involved in hydrogen peroxide catabolic process. Predicted to be located in cytoplasm. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PXDNL	NM_144651.5	c.165-11094A>G		intron_variant		ENST00000356297.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PXDNL	ENST00000356297.5	c.165-11094A>G		intron_variant		1	NM_144651.5	P1

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127967 AN: 152068 Hom.: 54163 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.826

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.842 AC: 128075 AN: 152186 Hom.: 54208 Cov.: 32 AF XY: 0.838 AC XY: 62385 AN XY: 74404

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.824

Alfa AF: 0.815 Hom.: 10286

Bravo AF: 0.853

Asia WGS AF: 0.810 AC: 2818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.78

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

LitVar

Other links and lift over

dbSNP: rs7012655; hg19: chr8-52578414;