chr2-62831106-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001142616.3(EHBP1):c.582A>G(p.Glu194=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000706 in 1,610,058 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00042 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00074 ( 21 hom. )
Consequence
EHBP1
NM_001142616.3 synonymous
NM_001142616.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.16
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 2-62831106-A-G is Benign according to our data. Variant chr2-62831106-A-G is described in ClinVar as [Benign]. Clinvar id is 3042677.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.16 with no splicing effect.
BS2
?
High AC in GnomAd at 65 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EHBP1 | NM_001142616.3 | c.582A>G | p.Glu194= | synonymous_variant | 7/23 | ENST00000431489.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EHBP1 | ENST00000431489.6 | c.582A>G | p.Glu194= | synonymous_variant | 7/23 | 1 | NM_001142616.3 | A1 | |
ENST00000452397.1 | n.67-4858T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000427 AC: 65AN: 152222Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00139 AC: 343AN: 246178Hom.: 3 AF XY: 0.00177 AC XY: 235AN XY: 133040
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GnomAD4 exome AF: 0.000736 AC: 1073AN: 1457718Hom.: 21 Cov.: 30 AF XY: 0.00103 AC XY: 746AN XY: 725040
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
EHBP1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 30, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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