10-98824158-C-T

Variant summary

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

The NM_021828.5(HPSE2):​c.611-80102G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,138 control chromosomes in the GnomAD database, including 49,163 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 0.80 ( 49163 hom., cov: 32)

Consequence

HPSE2
NM_021828.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.105
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HPSE2NM_021828.5 linkuse as main transcriptc.611-80102G>A intron_variant ENST00000370552.8 NP_068600.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HPSE2ENST00000370552.8 linkuse as main transcriptc.611-80102G>A intron_variant 1 NM_021828.5 ENSP00000359583 P1Q8WWQ2-1
HPSE2ENST00000370546.5 linkuse as main transcriptc.611-80102G>A intron_variant 1 ENSP00000359577 Q8WWQ2-2
HPSE2ENST00000370549.5 linkuse as main transcriptc.611-102330G>A intron_variant 1 ENSP00000359580 Q8WWQ2-3
HPSE2ENST00000628193.2 linkuse as main transcriptc.449-102330G>A intron_variant 1 ENSP00000485916 Q8WWQ2-4

Frequencies

GnomAD3 genomes
AF:
0.801
AC:
121786
AN:
152020
Hom.:
49111
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.825
Gnomad AMI
AF:
0.801
Gnomad AMR
AF:
0.713
Gnomad ASJ
AF:
0.794
Gnomad EAS
AF:
0.647
Gnomad SAS
AF:
0.820
Gnomad FIN
AF:
0.736
Gnomad MID
AF:
0.812
Gnomad NFE
AF:
0.827
Gnomad OTH
AF:
0.802
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.801
AC:
121895
AN:
152138
Hom.:
49163
Cov.:
32
AF XY:
0.794
AC XY:
59076
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.825
Gnomad4 AMR
AF:
0.713
Gnomad4 ASJ
AF:
0.794
Gnomad4 EAS
AF:
0.648
Gnomad4 SAS
AF:
0.821
Gnomad4 FIN
AF:
0.736
Gnomad4 NFE
AF:
0.828
Gnomad4 OTH
AF:
0.804
Alfa
AF:
0.817
Hom.:
79532
Bravo
AF:
0.798
Asia WGS
AF:
0.725
AC:
2525
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.7
DANN
Benign
0.46

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

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

Other links and lift over

dbSNP: rs2801405; hg19: chr10-100583915; API