rs2862507

Variant names:

• chr10-99048033-T-A
• rs2862507
• NM_021828.5:c.610+96205A>T

Your query was ambiguous. Multiple possible variants found:

• chr10-99048033-T-A
• chr10-99048033-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021828.5(HPSE2):​c.610+96205A>T variant causes a intron change. The variant allele was found at a frequency of 0.102 in 684,872 control chromosomes in the GnomAD database, including 4,258 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 0.10 (823 hom., cov: 32)
  • Exomes 𝑓: 0.10 (3435 hom.)
• Consequence: HPSE2 NM_021828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.68
• Publications: 0 publications found

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]

RPL7P36 (HGNC:37045): (ribosomal protein L7 pseudogene 36)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021828.5. 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
	HPSE2	NM_021828.5	MANE Select	c.610+96205A>T		intron	N/A	NP_068600.4
	HPSE2	NM_001166246.1		c.610+96205A>T		intron	N/A	NP_001159718.1	Q8WWQ2-2
	HPSE2	NM_001166244.1		c.610+96205A>T		intron	N/A	NP_001159716.1	Q8WWQ2-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HPSE2	ENST00000370552.8	TSL:1 MANE Select	c.610+96205A>T		intron	N/A	ENSP00000359583.3	Q8WWQ2-1
	HPSE2	ENST00000370546.5	TSL:1	c.610+96205A>T		intron	N/A	ENSP00000359577.1	Q8WWQ2-2
	HPSE2	ENST00000370549.5	TSL:1	c.610+96205A>T		intron	N/A	ENSP00000359580.1	Q8WWQ2-3

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15156 AN: 152118 Hom.: 822 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.0712

GnomAD4 exome AF: 0.103 AC: 55024 AN: 532636 Hom.: 3435 Cov.: 5 AF XY: 0.108 AC XY: 31033 AN XY: 287868

African (AFR) AF: 0.107 AC: 1610 AN: 15044

American (AMR) AF: 0.0317 AC: 1031 AN: 32502

Ashkenazi Jewish (ASJ) AF: 0.0466 AC: 850 AN: 18242

East Asian (EAS) AF: 0.122 AC: 3974 AN: 32568

South Asian (SAS) AF: 0.178 AC: 10583 AN: 59434

European-Finnish (FIN) AF: 0.119 AC: 3894 AN: 32690

Middle Eastern (MID) AF: 0.0571 AC: 127 AN: 2224

European-Non Finnish (NFE) AF: 0.0969 AC: 30112 AN: 310636

Other (OTH) AF: 0.0970 AC: 2843 AN: 29296

GnomAD4 genome AF: 0.0997 AC: 15175 AN: 152236 Hom.: 823 Cov.: 32 AF XY: 0.0996 AC XY: 7414 AN XY: 74452

African (AFR) AF: 0.110 AC: 4553 AN: 41550

American (AMR) AF: 0.0461 AC: 704 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3470

East Asian (EAS) AF: 0.143 AC: 739 AN: 5170

South Asian (SAS) AF: 0.183 AC: 886 AN: 4832

European-Finnish (FIN) AF: 0.118 AC: 1249 AN: 10612

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0980 AC: 6662 AN: 67998

Other (OTH) AF: 0.0705 AC: 149 AN: 2114

Alfa AF: 0.0524 Hom.: 53

Bravo AF: 0.0918

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	4.0
DANN	Benign	0.63
PhyloP100		5.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs2862507; hg19: chr10-100807790;