8-51665854-T-C

Variant names:

• chr8-51665854-T-C
• rs7012655
• NM_144651.5:c.165-11094A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144651.5. 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
	PXDNL	NM_144651.5	MANE Select	c.165-11094A>G		intron	N/A	NP_653252.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PXDNL	ENST00000356297.5	TSL:1 MANE Select	c.165-11094A>G		intron	N/A	ENSP00000348645.4	A1KZ92-1
	PXDNL	ENST00000894552.1		c.165-11094A>G		intron	N/A	ENSP00000564611.1
	PXDNL	ENST00000894549.1		c.165-11094A>G		intron	N/A	ENSP00000564608.1

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

African (AFR) AF: 0.930 AC: 38653 AN: 41548

American (AMR) AF: 0.846 AC: 12934 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3007 AN: 3470

East Asian (EAS) AF: 0.856 AC: 4431 AN: 5174

South Asian (SAS) AF: 0.835 AC: 4028 AN: 4824

European-Finnish (FIN) AF: 0.782 AC: 8265 AN: 10570

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53968 AN: 67992

Other (OTH) AF: 0.824 AC: 1741 AN: 2114

Alfa AF: 0.818 Hom.: 10624

Bravo AF: 0.853

Asia WGS AF: 0.810 AC: 2818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.78
PhyloP100		-0.0070
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: rs7012655; hg19: chr8-52578414;