1-22740019-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_017449.5(EPHB2):c.61+28976T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,808 control chromosomes in the GnomAD database, including 19,033 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 0.48 (19033 hom., cov: 33)
• Consequence: EPHB2 NM_017449.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHB2	NM_017449.5	c.61+28976T>C		intron_variant		ENST00000374630.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHB2	ENST00000374630.8	c.61+28976T>C		intron_variant		1	NM_017449.5	P4
EPHB2	ENST00000374632.7	c.61+28976T>C		intron_variant		1		A1
EPHB2	ENST00000400191.7	c.61+28976T>C		intron_variant		1
EPHB2	ENST00000544305.5	c.61+28976T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73169 AN: 151690 Hom.: 19002 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.483

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.482 AC: 73247 AN: 151808 Hom.: 19033 Cov.: 33 AF XY: 0.495 AC XY: 36669 AN XY: 74150

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.489

Alfa AF: 0.483 Hom.: 2971

Bravo AF: 0.476

Asia WGS AF: 0.778 AC: 2704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
Cadd	Benign	19
Dann	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1318720; hg19: chr1-23066512;