chr8-51372094-C-CA

Variant names:

• chr8-51372094-C-CA
• rs5891410
• NM_144651.5:c.3693-14dupT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_144651.5(PXDNL):​c.3693-14dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.57 (28922 hom., cov: 0)
  • Exomes 𝑓: 0.56 (121766 hom.)
  • Failed GnomAD Quality Control
• Consequence: PXDNL NM_144651.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.286
• Publications: 1 publications found

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 -10 ACMG points.

• BP6: Variant 8-51372094-C-CA is Benign according to our data. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-51372094-C-CA is described in CliVar as Benign. Clinvar id is 403354.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PXDNL	NM_144651.5	c.3693-14dupT		intron_variant	Intron 18 of 22	ENST00000356297.5	NP_653252.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PXDNL	ENST00000356297.5	c.3693-14dupT		intron_variant	Intron 18 of 22	1	NM_144651.5	ENSP00000348645.4
PXDNL	ENST00000522933.5	c.912-14dupT		intron_variant	Intron 1 of 5	5		ENSP00000428114.1
PXDNL	ENST00000522628.5	n.1491-14dupT		intron_variant	Intron 2 of 4	2		ENSP00000429855.1

Frequencies

GnomAD3 genomes AF: 0.567 AC: 84476 AN: 148862 Hom.: 28928 Cov.: 0

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.563

GnomAD2 exomes AF: 0.533 AC: 55851 AN: 104804 AF XY: 0.533

Gnomad AFR exome AF: 0.181

Gnomad AMR exome AF: 0.539

Gnomad ASJ exome AF: 0.526

Gnomad EAS exome AF: 0.521

Gnomad FIN exome AF: 0.618

Gnomad NFE exome AF: 0.556

Gnomad OTH exome AF: 0.528

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.565 AC: 633933 AN: 1122008 Hom.: 121766 Cov.: 28 AF XY: 0.565 AC XY: 313961 AN XY: 555832

African (AFR) AF: 0.138 AC: 3573 AN: 25866

American (AMR) AF: 0.544 AC: 15793 AN: 29030

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 10986 AN: 20688

East Asian (EAS) AF: 0.544 AC: 16577 AN: 30446

South Asian (SAS) AF: 0.537 AC: 35737 AN: 66608

European-Finnish (FIN) AF: 0.607 AC: 24791 AN: 40832

Middle Eastern (MID) AF: 0.460 AC: 2093 AN: 4552

European-Non Finnish (NFE) AF: 0.583 AC: 499013 AN: 856146

Other (OTH) AF: 0.530 AC: 25370 AN: 47840

GnomAD4 genome AF: 0.567 AC: 84464 AN: 148952 Hom.: 28922 Cov.: 0 AF XY: 0.574 AC XY: 41643 AN XY: 72610

African (AFR) AF: 0.146 AC: 5856 AN: 40094

American (AMR) AF: 0.673 AC: 10121 AN: 15036

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2328 AN: 3436

East Asian (EAS) AF: 0.661 AC: 3327 AN: 5034

South Asian (SAS) AF: 0.689 AC: 3250 AN: 4720

European-Finnish (FIN) AF: 0.764 AC: 7582 AN: 9928

Middle Eastern (MID) AF: 0.534 AC: 155 AN: 290

European-Non Finnish (NFE) AF: 0.740 AC: 49896 AN: 67444

Other (OTH) AF: 0.560 AC: 1154 AN: 2060

Alfa AF: 0.500 Hom.: 1994

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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: rs5891410; hg19: chr8-52284654; COSMIC: COSV62490765;