rs2862507

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.68
Variant links:
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)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HPSE2NM_021828.5 linkuse as main transcriptc.610+96205A>T intron_variant ENST00000370552.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HPSE2ENST00000370552.8 linkuse as main transcriptc.610+96205A>T intron_variant 1 NM_021828.5 P1Q8WWQ2-1
RPL7P36ENST00000444633.1 linkuse as main transcriptn.395T>A non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.0996
AC:
15156
AN:
152118
Hom.:
822
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR exome
AF:
0.107
Gnomad4 AMR exome
AF:
0.0317
Gnomad4 ASJ exome
AF:
0.0466
Gnomad4 EAS exome
AF:
0.122
Gnomad4 SAS exome
AF:
0.178
Gnomad4 FIN exome
AF:
0.119
Gnomad4 NFE exome
AF:
0.0969
Gnomad4 OTH exome
AF:
0.0970
GnomAD4 genome
AF:
0.0997
AC:
15175
AN:
152236
Hom.:
823
Cov.:
32
AF XY:
0.0996
AC XY:
7414
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.110
Gnomad4 AMR
AF:
0.0461
Gnomad4 ASJ
AF:
0.0467
Gnomad4 EAS
AF:
0.143
Gnomad4 SAS
AF:
0.183
Gnomad4 FIN
AF:
0.118
Gnomad4 NFE
AF:
0.0980
Gnomad4 OTH
AF:
0.0705
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 v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
CADD
Benign
4.0
DANN
Benign
0.63

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2862507; hg19: chr10-100807790; API