rs2018650
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001142616.3(EHBP1):c.*89T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,112,730 control chromosomes in the GnomAD database, including 10,448 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 0.11 ( 1281 hom., cov: 32)
Exomes 𝑓: 0.13 ( 9167 hom. )
Consequence
EHBP1
NM_001142616.3 3_prime_UTR
NM_001142616.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.431
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EHBP1 | NM_001142616.3 | c.*89T>C | 3_prime_UTR_variant | 23/23 | ENST00000431489.6 | ||
EHBP1-AS1 | NR_033389.1 | n.408-146A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EHBP1 | ENST00000431489.6 | c.*89T>C | 3_prime_UTR_variant | 23/23 | 1 | NM_001142616.3 | A1 | ||
EHBP1-AS1 | ENST00000650490.1 | n.387+893A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.113 AC: 17266AN: 152128Hom.: 1284 Cov.: 32
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GnomAD4 exome AF: 0.130 AC: 124935AN: 960484Hom.: 9167 Cov.: 12 AF XY: 0.132 AC XY: 64175AN XY: 487706
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GnomAD4 genome ? AF: 0.113 AC: 17261AN: 152246Hom.: 1281 Cov.: 32 AF XY: 0.118 AC XY: 8760AN XY: 74438
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ClinVar
Not reported inComputational 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