rs150803261
Positions:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_ModerateBP6_Moderate
The NM_017449.5(EPHB2):c.787G>A(p.Val263Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000428 in 1,613,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000092 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000038 ( 0 hom. )
Consequence
EPHB2
NM_017449.5 missense
NM_017449.5 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 4.51
Genes affected
EPHB2 (HGNC:3393): (EPH receptor B2) This gene encodes a member of the Eph receptor family of receptor tyrosine kinase transmembrane glycoproteins. These receptors are composed of an N-terminal glycosylated ligand-binding domain, a transmembrane region and an intracellular kinase domain. They bind ligands called ephrins and are involved in diverse cellular processes including motility, division, and differentiation. A distinguishing characteristic of Eph-ephrin signaling is that both receptors and ligands are competent to transduce a signaling cascade, resulting in bidirectional signaling. This protein belongs to a subgroup of the Eph receptors called EphB. Proteins of this subgroup are distinguished from other members of the family by sequence homology and preferential binding affinity for membrane-bound ephrin-B ligands. Allelic variants are associated with prostate and brain cancer susceptibility. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, EPHB2
BP4
?
Computational evidence support a benign effect (MetaRNN=0.14827463).
BP6
?
Variant 1-22785052-G-A is Benign according to our data. Variant chr1-22785052-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 221961.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHB2 | NM_017449.5 | c.787G>A | p.Val263Ile | missense_variant | 3/16 | ENST00000374630.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHB2 | ENST00000374630.8 | c.787G>A | p.Val263Ile | missense_variant | 3/16 | 1 | NM_017449.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152260Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000719 AC: 18AN: 250372Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135660
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GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461242Hom.: 0 Cov.: 32 AF XY: 0.0000454 AC XY: 33AN XY: 726946
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GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152378Hom.: 0 Cov.: 33 AF XY: 0.0000939 AC XY: 7AN XY: 74518
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Irido-corneo-trabecular dysgenesis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Paul Sabatier University EA-4555, Paul Sabatier University | Jan 01, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
0.88, 0.043
.;.;P;B;.
Vest4
MVP
MPC
0.48
ClinPred
T
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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