13-106507098-G-T

Variant names:

• chr13-106507098-G-T
• rs7983579
• NM_004093.4:c.406+5431C>A

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+5431C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,900 control chromosomes in the GnomAD database, including 21,618 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 (21618 hom., cov: 31)
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 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+5431C>A		intron	N/A	NP_004084.1	P52799
	EFNB2	NM_001372056.1		c.406+5431C>A		intron	N/A	NP_001358985.1
	EFNB2	NM_001372057.1		c.406+5431C>A		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+5431C>A		intron	N/A	ENSP00000493716.1	P52799
	EFNB2	ENST00000955444.1		c.406+5431C>A		intron	N/A	ENSP00000625503.1
	ENSG00000284966	ENST00000642447.1		n.86-2721G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80529 AN: 151782 Hom.: 21598 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.530 AC: 80579 AN: 151900 Hom.: 21618 Cov.: 31 AF XY: 0.533 AC XY: 39532 AN XY: 74204

African (AFR) AF: 0.466 AC: 19295 AN: 41432

American (AMR) AF: 0.515 AC: 7864 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1531 AN: 3468

East Asian (EAS) AF: 0.564 AC: 2907 AN: 5152

South Asian (SAS) AF: 0.493 AC: 2378 AN: 4824

European-Finnish (FIN) AF: 0.613 AC: 6446 AN: 10522

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38453 AN: 67928

Other (OTH) AF: 0.514 AC: 1086 AN: 2112

Alfa AF: 0.528 Hom.: 11192

Bravo AF: 0.518

Asia WGS AF: 0.531 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		1.1
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: rs7983579; hg19: chr13-107159446;