8-51372094-CA-CAAAAAA

Variant names:

• chr8-51372094-C-CAAAAA
• rs5891410
• NM_144651.5:c.3693-18_3693-14dupTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_144651.5(PXDNL):​c.3693-18_3693-14dupTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PXDNL NM_144651.5 intron
• Clinical Significance: Not reported in ClinVar
• 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: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PXDNL	NM_144651.5	c.3693-18_3693-14dupTTTTT		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.3693-18_3693-14dupTTTTT		intron_variant	Intron 18 of 22	1	NM_144651.5	ENSP00000348645.4
PXDNL	ENST00000522933.5	c.912-18_912-14dupTTTTT		intron_variant	Intron 1 of 5	5		ENSP00000428114.1
PXDNL	ENST00000522628.5	n.1491-18_1491-14dupTTTTT		intron_variant	Intron 2 of 4	2		ENSP00000429855.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 148924 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000191 AC: 2 AN: 104804 AF XY: 0.0000181

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000129

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000243

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1131840 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 560740

African (AFR) AF: 0.00 AC: 0 AN: 27382

American (AMR) AF: 0.00 AC: 0 AN: 29352

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20928

East Asian (EAS) AF: 0.00 AC: 0 AN: 30782

South Asian (SAS) AF: 0.00 AC: 0 AN: 67322

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41054

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4606

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 862040

Other (OTH) AF: 0.00 AC: 0 AN: 48374

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 148924 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 72554

African (AFR) AF: 0.00 AC: 0 AN: 40004

American (AMR) AF: 0.00 AC: 0 AN: 15028

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3438

East Asian (EAS) AF: 0.00 AC: 0 AN: 5052

South Asian (SAS) AF: 0.00 AC: 0 AN: 4742

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9926

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67468

Other (OTH) AF: 0.00 AC: 0 AN: 2042

Alfa AF: 0.000370 Hom.: 1994

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs5891410; hg19: chr8-52284654;