7-100823256-C-T

Position:

• chr7-100823256-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004444.5(EPHB4):​c.411+388G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,032 control chromosomes in the GnomAD database, including 4,766 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 0.23 (4766 hom., cov: 32)
• Consequence: EPHB4 NM_004444.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621

Genes affected

EPHB4 (HGNC:3395): (EPH receptor B4) Ephrin receptors and their ligands, the ephrins, mediate numerous developmental processes, particularly in the nervous system. Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. The Eph family of receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. Ephrin receptors make up the largest subgroup of the receptor tyrosine kinase (RTK) family. The protein encoded by this gene binds to ephrin-B2 and plays an essential role in vascular development. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPHB4	NM_004444.5	c.411+388G>A		intron_variant		ENST00000358173.8	NP_004435.3
EPHB4	XM_017011816.2	c.411+388G>A		intron_variant			XP_016867305.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPHB4	ENST00000358173.8	c.411+388G>A		intron_variant		1	NM_004444.5	ENSP00000350896	P1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35593 AN: 151914 Hom.: 4776 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.0364

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.234 AC: 35578 AN: 152032 Hom.: 4766 Cov.: 32 AF XY: 0.233 AC XY: 17314 AN XY: 74312

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.0359

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.256

Alfa AF: 0.168 Hom.: 300

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.71
DANN	Benign	0.91

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs314308; hg19: chr7-100420878;