rs17470570

chr10-98820366-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021828.5(HPSE2):c.611-76310T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0426 in 152,274 control chromosomes in the GnomAD database, including 197 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 0.043 (197 hom., cov: 32)
• Consequence: HPSE2 NM_021828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HPSE2	NM_021828.5	c.611-76310T>C		intron_variant		ENST00000370552.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HPSE2	ENST00000370552.8	c.611-76310T>C		intron_variant		1	NM_021828.5	P1
HPSE2	ENST00000370546.5	c.611-76310T>C		intron_variant		1
HPSE2	ENST00000370549.5	c.611-98538T>C		intron_variant		1
HPSE2	ENST00000628193.2	c.449-98538T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6486 AN: 152156 Hom.: 197 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0238

Gnomad ASJ AF: 0.0188

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.0353

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

GnomAD4 genome AF: 0.0426 AC: 6486 AN: 152274 Hom.: 197 Cov.: 32 AF XY: 0.0405 AC XY: 3014 AN XY: 74466

Gnomad4 AFR AF: 0.0109

Gnomad4 AMR AF: 0.0237

Gnomad4 ASJ AF: 0.0188

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0444

Gnomad4 FIN AF: 0.0476

Gnomad4 NFE AF: 0.0697

Gnomad4 OTH AF: 0.0340

Alfa AF: 0.0544 Hom.: 53

Bravo AF: 0.0376

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.71
Dann	Benign	0.38

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: rs17470570; hg19: chr10-100580123;