chr13-106510595-A-G

Variant names:

• chr13-106510595-A-G
• rs11840214
• NM_004093.4:c.406+1934T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004093.4(EFNB2):​c.406+1934T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,478 control chromosomes in the GnomAD database, including 4,797 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 0.20 (4797 hom., cov: 33)
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 5 publications found

Genes affected

EFNB2 (HGNC:3227): (ephrin B2) This gene encodes a member of the ephrin (EPH) family. The ephrins and EPH-related receptors comprise the largest subfamily of receptor protein-tyrosine kinases and have been implicated in mediating developmental events, especially in the nervous system and in erythropoiesis. 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. This gene encodes an EFNB class ephrin which binds to the EPHB4 and EPHA3 receptors. [provided by RefSeq, Jul 2008]

ENSG00000284966 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004093.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFNB2	NM_004093.4	MANE Select	c.406+1934T>C		intron	N/A	NP_004084.1	P52799
	EFNB2	NM_001372056.1		c.406+1934T>C		intron	N/A	NP_001358985.1
	EFNB2	NM_001372057.1		c.406+1934T>C		intron	N/A	NP_001358986.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFNB2	ENST00000646441.1	MANE Select	c.406+1934T>C		intron	N/A	ENSP00000493716.1	P52799
	EFNB2	ENST00000955444.1		c.406+1934T>C		intron	N/A	ENSP00000625503.1
	EFNB2	ENST00000643990.1		n.10+5843T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31000 AN: 151360 Hom.: 4781 Cov.: 33

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.0969

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.205 AC: 31048 AN: 151478 Hom.: 4797 Cov.: 33 AF XY: 0.199 AC XY: 14732 AN XY: 74060

African (AFR) AF: 0.432 AC: 17626 AN: 40826

American (AMR) AF: 0.118 AC: 1795 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 588 AN: 3470

East Asian (EAS) AF: 0.00675 AC: 35 AN: 5184

South Asian (SAS) AF: 0.0970 AC: 468 AN: 4826

European-Finnish (FIN) AF: 0.132 AC: 1401 AN: 10592

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8631 AN: 68002

Other (OTH) AF: 0.174 AC: 368 AN: 2110

Alfa AF: 0.138 Hom.: 2364

Bravo AF: 0.212

Asia WGS AF: 0.0810 AC: 283 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.36
PhyloP100		-0.24
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11840214; hg19: chr13-107162943;