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10-98459557-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_021828.5(HPSE2):​c.*17C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 1,611,968 control chromosomes in the GnomAD database, including 200,666 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 21421 hom., cov: 32)
Exomes 𝑓: 0.49 ( 179245 hom. )

Consequence

HPSE2
NM_021828.5 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.310
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 10-98459557-G-A is Benign according to our data. Variant chr10-98459557-G-A is described in ClinVar as [Benign]. Clinvar id is 1228841.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-98459557-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HPSE2NM_021828.5 linkuse as main transcriptc.*17C>T 3_prime_UTR_variant 12/12 ENST00000370552.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HPSE2ENST00000370552.8 linkuse as main transcriptc.*17C>T 3_prime_UTR_variant 12/121 NM_021828.5 P1Q8WWQ2-1

Frequencies

GnomAD3 genomes
AF:
0.527
AC:
79943
AN:
151828
Hom.:
21407
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.615
Gnomad AMI
AF:
0.485
Gnomad AMR
AF:
0.511
Gnomad ASJ
AF:
0.660
Gnomad EAS
AF:
0.530
Gnomad SAS
AF:
0.453
Gnomad FIN
AF:
0.447
Gnomad MID
AF:
0.494
Gnomad NFE
AF:
0.487
Gnomad OTH
AF:
0.549
GnomAD3 exomes
AF:
0.504
AC:
126674
AN:
251114
Hom.:
32320
AF XY:
0.499
AC XY:
67754
AN XY:
135828
show subpopulations
Gnomad AFR exome
AF:
0.618
Gnomad AMR exome
AF:
0.512
Gnomad ASJ exome
AF:
0.663
Gnomad EAS exome
AF:
0.539
Gnomad SAS exome
AF:
0.444
Gnomad FIN exome
AF:
0.461
Gnomad NFE exome
AF:
0.490
Gnomad OTH exome
AF:
0.520
GnomAD4 exome
AF:
0.494
AC:
720560
AN:
1460022
Hom.:
179245
Cov.:
36
AF XY:
0.491
AC XY:
357041
AN XY:
726438
show subpopulations
Gnomad4 AFR exome
AF:
0.626
Gnomad4 AMR exome
AF:
0.514
Gnomad4 ASJ exome
AF:
0.659
Gnomad4 EAS exome
AF:
0.565
Gnomad4 SAS exome
AF:
0.439
Gnomad4 FIN exome
AF:
0.474
Gnomad4 NFE exome
AF:
0.486
Gnomad4 OTH exome
AF:
0.508
GnomAD4 genome
AF:
0.527
AC:
80012
AN:
151946
Hom.:
21421
Cov.:
32
AF XY:
0.524
AC XY:
38894
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.615
Gnomad4 AMR
AF:
0.511
Gnomad4 ASJ
AF:
0.660
Gnomad4 EAS
AF:
0.530
Gnomad4 SAS
AF:
0.454
Gnomad4 FIN
AF:
0.447
Gnomad4 NFE
AF:
0.487
Gnomad4 OTH
AF:
0.545
Alfa
AF:
0.510
Hom.:
20558
Bravo
AF:
0.541
Asia WGS
AF:
0.523
AC:
1822
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxNov 12, 2018- -
Urofacial syndrome type 1 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabAug 10, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
8.3
DANN
Benign
0.73

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: rs10883099; hg19: chr10-100219314; COSMIC: COSV65184032; COSMIC: COSV65184032; API