rs721048
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5BP4BA1
The NM_001142616.3(EHBP1):c.1185+30064G>A 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 152,112 control chromosomes in the GnomAD database, including 1,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.13 ( 1698 hom., cov: 31)
Consequence
EHBP1
NM_001142616.3 intron
NM_001142616.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.575
Genes affected
EHBP1 (HGNC:29144): (EH domain binding protein 1) This gene encodes an Eps15 homology domain binding protein. The encoded protein may play a role in endocytic trafficking. A single nucleotide polymorphism in this gene is associated with an aggressive form of prostate cancer. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PP5
Variant 2-62904596-G-A is Pathogenic according to our data. Variant chr2-62904596-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 1364.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83). . Strength limited to SUPPORTING due to the PP5.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EHBP1 | NM_001142616.3 | c.1185+30064G>A | intron_variant | ENST00000431489.6 | NP_001136088.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EHBP1 | ENST00000431489.6 | c.1185+30064G>A | intron_variant | 1 | NM_001142616.3 | ENSP00000403783 | A1 | |||
EHBP1 | ENST00000263991.9 | c.1290+30064G>A | intron_variant | 1 | ENSP00000263991 | P3 | ||||
EHBP1 | ENST00000405289.5 | c.1185+30064G>A | intron_variant | 1 | ENSP00000385524 | A1 | ||||
EHBP1 | ENST00000405015.7 | c.1185+30064G>A | intron_variant | 2 | ENSP00000384143 | A1 |
Frequencies
GnomAD3 genomes AF: 0.133 AC: 20219AN: 151994Hom.: 1697 Cov.: 31
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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: 20208AN: 152112Hom.: 1698 Cov.: 31 AF XY: 0.133 AC XY: 9868AN XY: 74366
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Prostate cancer, hereditary, 12 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2008 | - - |
Computational scores
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Name
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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