rs12507864
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000311412.10(HPSE):c.227+1215A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,156 control chromosomes in the GnomAD database, including 1,791 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 0.13 ( 1791 hom., cov: 32)
Consequence
HPSE
ENST00000311412.10 intron
ENST00000311412.10 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.794
Genes affected
HPSE (HGNC:5164): (heparanase) Heparan sulfate proteoglycans are major components of the basement membrane and extracellular matrix. The protein encoded by this gene is an enzyme that cleaves heparan sulfate proteoglycans to permit cell movement through remodeling of the extracellular matrix. In addition, this cleavage can release bioactive molecules from the extracellular matrix. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HPSE | NM_001098540.3 | c.227+1215A>G | intron_variant | ENST00000311412.10 | NP_001092010.1 | |||
HPSE | NM_001166498.3 | c.227+1215A>G | intron_variant | NP_001159970.1 | ||||
HPSE | NM_001199830.1 | c.227+1215A>G | intron_variant | NP_001186759.1 | ||||
HPSE | NM_006665.6 | c.227+1215A>G | intron_variant | NP_006656.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HPSE | ENST00000311412.10 | c.227+1215A>G | intron_variant | 1 | NM_001098540.3 | ENSP00000308107 | P1 |
Frequencies
GnomAD3 genomes AF: 0.133 AC: 20184AN: 152038Hom.: 1784 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.133 AC: 20216AN: 152156Hom.: 1791 Cov.: 32 AF XY: 0.132 AC XY: 9803AN XY: 74408
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293
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at