chr3-134930036-TGCCCCATCCAGAG-T

Position:

• chr3-134930036-TGCCCCATCCAGAG-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_004441.5(EPHB1):​c.123+4158_123+4170del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (28613 hom., cov: 0)
• Consequence: EPHB1 NM_004441.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

Genes affected

EPHB1 (HGNC:3392): (EPH receptor B1) 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 is a receptor for ephrin-B family members. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHB1	NM_004441.5	c.123+4158_123+4170del		intron_variant		ENST00000398015.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHB1	ENST00000398015.8	c.123+4158_123+4170del		intron_variant		1	NM_004441.5	P1

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89357 AN: 151770 Hom.: 28573 Cov.: 0

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.589 AC: 89450 AN: 151888 Hom.: 28613 Cov.: 0 AF XY: 0.584 AC XY: 43386 AN XY: 74258

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.575

Alfa AF: 0.537 Hom.: 2846

Bravo AF: 0.596

Asia WGS AF: 0.618 AC: 2149 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2067188; hg19: chr3-134648878;