13-106494162-G-A

Variant names:

• chr13-106494162-G-A
• rs4399422
• NM_004093.4:c.613+719C>T

Variant summary

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

The NM_004093.4(EFNB2):​c.613+719C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,020 control chromosomes in the GnomAD database, including 15,320 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 0.44 (15320 hom., cov: 33)
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.69
• Publications: 1 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=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFNB2	NM_004093.4	MANE Select	c.613+719C>T		intron	N/A	NP_004084.1
	EFNB2	NM_001372056.1		c.520+719C>T		intron	N/A	NP_001358985.1
	EFNB2	NM_001372057.1		c.500-734C>T		intron	N/A	NP_001358986.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFNB2	ENST00000646441.1	MANE Select	c.613+719C>T		intron	N/A	ENSP00000493716.1
	ENSG00000284966	ENST00000649449.1		n.1804G>A		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000284966	ENST00000666523.1		n.1613G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67269 AN: 151900 Hom.: 15282 Cov.: 33

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.443 AC: 67359 AN: 152020 Hom.: 15320 Cov.: 33 AF XY: 0.442 AC XY: 32805 AN XY: 74292

African (AFR) AF: 0.530 AC: 21991 AN: 41468

American (AMR) AF: 0.458 AC: 6998 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1770 AN: 3472

East Asian (EAS) AF: 0.432 AC: 2231 AN: 5160

South Asian (SAS) AF: 0.504 AC: 2427 AN: 4820

European-Finnish (FIN) AF: 0.350 AC: 3692 AN: 10544

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26726 AN: 67960

Other (OTH) AF: 0.460 AC: 971 AN: 2110

Alfa AF: 0.429 Hom.: 18257

Bravo AF: 0.457

Asia WGS AF: 0.461 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.67
PhyloP100		2.7
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: rs4399422; hg19: chr13-107146510;