rs11840214

chr13-106510595-A-Gchr13-106510595-A-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFNB2	NM_004093.4	c.406+1934T>C		intron_variant		ENST00000646441.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFNB2	ENST00000646441.1	c.406+1934T>C		intron_variant			NM_004093.4	P1
	ENST00000646480.1	n.497-5538A>G		intron_variant, non_coding_transcript_variant
EFNB2	ENST00000643990.1	n.10+5843T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.00675

Gnomad4 SAS AF: 0.0970

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.174

Alfa AF: 0.136 Hom.: 1946

Bravo AF: 0.212

Asia WGS AF: 0.0810 AC: 283 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.1
Dann	Benign	0.36

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: rs11840214; hg19: chr13-107162943;