10-98459926-AC-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_021828.5(HPSE2):c.1614-188del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.53 (21414 hom., cov: 0)
• Consequence: HPSE2 NM_021828.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.63

Genes affected

HPSE2 (HGNC:18374): (heparanase 2 (inactive)) This gene encodes a heparanase enzyme. The encoded protein is a endoglycosidase that degrades heparin sulfate proteoglycans located on the extracellular matrix and cell surface. This protein may be involved in biological processes involving remodeling of the extracellular matrix including angiogenesis and tumor progression. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-98459926-AC-A is Benign according to our data. Variant chr10-98459926-AC-A is described in ClinVar as [Benign]. Clinvar id is 1259787.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HPSE2	NM_021828.5	c.1614-188del		intron_variant		ENST00000370552.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HPSE2	ENST00000370552.8	c.1614-188del		intron_variant		1	NM_021828.5	P1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 79868 AN: 151110 Hom.: 21400 Cov.: 0

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.550

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.529 AC: 79936 AN: 151230 Hom.: 21414 Cov.: 0 AF XY: 0.526 AC XY: 38838 AN XY: 73854

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.546

Asia WGS AF: 0.532 AC: 1854 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs34700526; hg19: chr10-100219683;