13-106515142-G-T

Variant names:

• chr13-106515142-G-T
• rs9520091
• NM_004093.4:c.123-2330C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004093.4(EFNB2):​c.123-2330C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,130 control chromosomes in the GnomAD database, including 51,284 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 0.81 (51284 hom., cov: 32)
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFNB2	NM_004093.4	c.123-2330C>A		intron_variant	Intron 1 of 4	ENST00000646441.1	NP_004084.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFNB2	ENST00000646441.1	c.123-2330C>A		intron_variant	Intron 1 of 4		NM_004093.4	ENSP00000493716.1
EFNB2	ENST00000643990.1	n.10+1296C>A		intron_variant	Intron 1 of 3
ENSG00000284966	ENST00000646480.1	n.497-991G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123196 AN: 152012 Hom.: 51259 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.810 AC: 123267 AN: 152130 Hom.: 51284 Cov.: 32 AF XY: 0.814 AC XY: 60501 AN XY: 74352

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.875

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.847

Alfa AF: 0.880 Hom.: 10116

Bravo AF: 0.788

Asia WGS AF: 0.806 AC: 2804 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.76
DANN	Benign	0.70

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: rs9520091; hg19: chr13-107167490;