8-51372094-CA-CAAA

Position:

• chr8-51372094-CA-CAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_144651.5(PXDNL):​c.3693-15_3693-14dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 1,179,802 control chromosomes in the GnomAD database, including 5 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0018 (2 hom., cov: 0)
  • Exomes 𝑓: 0.025 (3 hom.)
• Consequence: PXDNL NM_144651.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

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 -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.051 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PXDNL	NM_144651.5	c.3693-15_3693-14dupTT		intron_variant		ENST00000356297.5	NP_653252.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PXDNL	ENST00000356297.5	c.3693-14_3693-13insTT		intron_variant		1	NM_144651.5	ENSP00000348645.4
PXDNL	ENST00000522933.5	c.912-14_912-13insTT		intron_variant		5		ENSP00000428114.1
PXDNL	ENST00000522628.5	n.1491-14_1491-13insTT		intron_variant		2		ENSP00000429855.1

Frequencies

GnomAD3 genomes AF: 0.00179 AC: 266 AN: 148832 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.000725

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0137

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000198

Gnomad SAS AF: 0.00169

Gnomad FIN AF: 0.000404

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000237

Gnomad OTH AF: 0.000979

GnomAD3 exomes AF: 0.0296 AC: 3098 AN: 104804 Hom.: 0 AF XY: 0.0302 AC XY: 1672 AN XY: 55320

Gnomad AFR exome AF: 0.000381

Gnomad AMR exome AF: 0.0615

Gnomad ASJ exome AF: 0.0255

Gnomad EAS exome AF: 0.0181

Gnomad SAS exome AF: 0.0305

Gnomad FIN exome AF: 0.0201

Gnomad NFE exome AF: 0.0263

Gnomad OTH exome AF: 0.0223

GnomAD4 exome AF: 0.0245 AC: 25301 AN: 1030880 Hom.: 3 Cov.: 28 AF XY: 0.0241 AC XY: 12291 AN XY: 509510

Gnomad4 AFR exome AF: 0.00110

Gnomad4 AMR exome AF: 0.0533

Gnomad4 ASJ exome AF: 0.0198

Gnomad4 EAS exome AF: 0.0134

Gnomad4 SAS exome AF: 0.0185

Gnomad4 FIN exome AF: 0.0162

Gnomad4 NFE exome AF: 0.0261

Gnomad4 OTH exome AF: 0.0198

GnomAD4 genome AF: 0.00180 AC: 268 AN: 148922 Hom.: 2 Cov.: 0 AF XY: 0.00207 AC XY: 150 AN XY: 72604

Gnomad4 AFR AF: 0.000723

Gnomad4 AMR AF: 0.0138

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000198

Gnomad4 SAS AF: 0.00169

Gnomad4 FIN AF: 0.000404

Gnomad4 NFE AF: 0.000237

Gnomad4 OTH AF: 0.000970

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5891410; hg19: chr8-52284654;