3-134930036-TGCCCCATCCAGAG-T

Variant names:

• chr3-134930036-TGCCCCATCCAGAG-T
• rs2067188
• NM_004441.5:c.123+4158_123+4170delCCCCATCCAGAGG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_004441.5(EPHB1):​c.123+4158_123+4170delCCCCATCCAGAGG variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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
• Publications: 2 publications found

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]

ENSG00000288700 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
EPHB1	NM_004441.5	c.123+4158_123+4170delCCCCATCCAGAGG		intron_variant	Intron 2 of 15	ENST00000398015.8	NP_004432.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHB1	ENST00000398015.8	c.123+4157_123+4169delGCCCCATCCAGAG		intron_variant	Intron 2 of 15	1	NM_004441.5	ENSP00000381097.3

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

African (AFR) AF: 0.857 AC: 35522 AN: 41454

American (AMR) AF: 0.442 AC: 6751 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1935 AN: 3460

East Asian (EAS) AF: 0.533 AC: 2730 AN: 5124

South Asian (SAS) AF: 0.667 AC: 3216 AN: 4820

European-Finnish (FIN) AF: 0.428 AC: 4530 AN: 10590

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 32957 AN: 67866

Other (OTH) AF: 0.575 AC: 1211 AN: 2106

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

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2067188; hg19: chr3-134648878;