13-106508277-T-C

Variant names:

• chr13-106508277-T-C
• rs9514543
• NM_004093.4:c.406+4252A>G

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+4252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,890 control chromosomes in the GnomAD database, including 21,419 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 0.53 (21419 hom., cov: 31)
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 0 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFNB2	NM_004093.4	c.406+4252A>G		intron_variant	Intron 2 of 4	ENST00000646441.1	NP_004084.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFNB2	ENST00000646441.1	c.406+4252A>G		intron_variant	Intron 2 of 4		NM_004093.4	ENSP00000493716.1
ENSG00000284966	ENST00000642447.1	n.86-1542T>C		intron_variant	Intron 1 of 1
EFNB2	ENST00000643990.1	n.10+8161A>G		intron_variant	Intron 1 of 3
ENSG00000284966	ENST00000646480.1	n.497-7856T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79782 AN: 151772 Hom.: 21400 Cov.: 31

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.526 AC: 79842 AN: 151890 Hom.: 21419 Cov.: 31 AF XY: 0.529 AC XY: 39250 AN XY: 74224

African (AFR) AF: 0.438 AC: 18147 AN: 41416

American (AMR) AF: 0.514 AC: 7853 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3470

East Asian (EAS) AF: 0.566 AC: 2912 AN: 5142

South Asian (SAS) AF: 0.516 AC: 2478 AN: 4806

European-Finnish (FIN) AF: 0.629 AC: 6622 AN: 10536

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.567 AC: 38551 AN: 67942

Other (OTH) AF: 0.504 AC: 1061 AN: 2104

Alfa AF: 0.544 Hom.: 2768

Bravo AF: 0.510

Asia WGS AF: 0.544 AC: 1888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.42
PhyloP100		0.19
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: rs9514543; hg19: chr13-107160625;