rs141024159

Variant names:

• chr8-51408678-G-A
• rs141024159
• NM_144651.5:c.2946C>T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BS1 BS2

The NM_144651.5(PXDNL):​c.2946C>T​(p.Ala982Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0129 in 1,600,496 control chromosomes in the GnomAD database, including 167 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.011 (11 hom., cov: 33)
  • Exomes 𝑓: 0.013 (156 hom.)
• Consequence: PXDNL NM_144651.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.725

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

Our verdict: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.015).
• BP6: Variant 8-51408678-G-A is Benign according to our data. Variant chr8-51408678-G-A is described in ClinVar as [Benign]. Clinvar id is 403355.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.725 with no splicing effect.
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0115 (1747/152272) while in subpopulation NFE AF = 0.0161 (1095/68010). AF 95% confidence interval is 0.0153. There are 11 homozygotes in GnomAd4. There are 890 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PXDNL	NM_144651.5	c.2946C>T	p.Ala982Ala	synonymous_variant	Exon 17 of 23	ENST00000356297.5	NP_653252.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PXDNL	ENST00000356297.5	c.2946C>T	p.Ala982Ala	synonymous_variant	Exon 17 of 23	1	NM_144651.5	ENSP00000348645.4
PXDNL	ENST00000522933.5	c.300C>T	p.Ala100Ala	synonymous_variant	Exon 1 of 6	5		ENSP00000428114.1
PXDNL	ENST00000522628.5	n.744C>T		non_coding_transcript_exon_variant	Exon 1 of 5	2		ENSP00000429855.1

Frequencies

GnomAD3 genomes AF: 0.0115 AC: 1748 AN: 152154 Hom.: 11 Cov.: 33

Gnomad AFR AF: 0.00203

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.00896

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00538

Gnomad FIN AF: 0.0285

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0161

Gnomad OTH AF: 0.0129

GnomAD2 exomes AF: 0.0120 AC: 2645 AN: 221266 AF XY: 0.0120

Gnomad AFR exome AF: 0.00162

Gnomad AMR exome AF: 0.00656

Gnomad ASJ exome AF: 0.0163

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0293

Gnomad NFE exome AF: 0.0149

Gnomad OTH exome AF: 0.0133

GnomAD4 exome AF: 0.0130 AC: 18866 AN: 1448224 Hom.: 156 Cov.: 31 AF XY: 0.0130 AC XY: 9340 AN XY: 719268

Gnomad4 AFR exome AF: 0.00165 AC: 55 AN: 33238

Gnomad4 AMR exome AF: 0.00647 AC: 277 AN: 42812

Gnomad4 ASJ exome AF: 0.0153 AC: 394 AN: 25816

Gnomad4 EAS exome AF: 0.0000256 AC: 1 AN: 38996

Gnomad4 SAS exome AF: 0.00560 AC: 472 AN: 84286

Gnomad4 FIN exome AF: 0.0287 AC: 1496 AN: 52156

Gnomad4 NFE exome AF: 0.0139 AC: 15393 AN: 1105302

Gnomad4 Remaining exome AF: 0.0116 AC: 694 AN: 59864

GnomAD4 genome AF: 0.0115 AC: 1747 AN: 152272 Hom.: 11 Cov.: 33 AF XY: 0.0120 AC XY: 890 AN XY: 74442

Gnomad4 AFR AF: 0.00202 AC: 0.00202117 AN: 0.00202117

Gnomad4 AMR AF: 0.00895 AC: 0.00894957 AN: 0.00894957

Gnomad4 ASJ AF: 0.0167 AC: 0.0167051 AN: 0.0167051

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00539 AC: 0.00538748 AN: 0.00538748

Gnomad4 FIN AF: 0.0285 AC: 0.0285472 AN: 0.0285472

Gnomad4 NFE AF: 0.0161 AC: 0.0161006 AN: 0.0161006

Gnomad4 OTH AF: 0.0128 AC: 0.0127599 AN: 0.0127599

Alfa AF: 0.0136 Hom.: 4

Bravo AF: 0.00935

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency, silent variant -

PXDNL-related disorder Benign:1

Oct 14, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.51
Mutation Taster		=98/2	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

Publications

LitVar

Other links and lift over

dbSNP: rs141024159; hg19: chr8-52321238;