13-106508609-G-C

Variant names:

• chr13-106508609-G-C
• rs8001826
• NM_004093.4:c.406+3920C>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+3920C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,144 control chromosomes in the GnomAD database, including 2,467 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 0.16 (2467 hom., cov: 33)
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFNB2	NM_004093.4	c.406+3920C>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+3920C>G		intron_variant	Intron 2 of 4		NM_004093.4	ENSP00000493716.1
ENSG00000284966	ENST00000642447.1	n.86-1210G>C		intron_variant	Intron 1 of 1
EFNB2	ENST00000643990.1	n.10+7829C>G		intron_variant	Intron 1 of 3
ENSG00000284966	ENST00000646480.1	n.497-7524G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24681 AN: 152026 Hom.: 2463 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00694

Gnomad SAS AF: 0.0900

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.162 AC: 24691 AN: 152144 Hom.: 2467 Cov.: 33 AF XY: 0.159 AC XY: 11832 AN XY: 74386

African (AFR) AF: 0.278 AC: 11550 AN: 41480

American (AMR) AF: 0.104 AC: 1588 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3470

East Asian (EAS) AF: 0.00696 AC: 36 AN: 5176

South Asian (SAS) AF: 0.0897 AC: 432 AN: 4818

European-Finnish (FIN) AF: 0.136 AC: 1442 AN: 10578

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8597 AN: 68006

Other (OTH) AF: 0.145 AC: 307 AN: 2110

Alfa AF: 0.0561 Hom.: 54

Bravo AF: 0.165

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.48
PhyloP100		0.038
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs8001826; hg19: chr13-107160957;