rs9520092

chr13-106515191-C-T

Variant summary

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

The NM_004093.4(EFNB2):c.123-2379G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,984 control chromosomes in the GnomAD database, including 22,763 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 (22763 hom., cov: 32)
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFNB2	NM_004093.4	c.123-2379G>A		intron_variant		ENST00000646441.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFNB2	ENST00000646441.1	c.123-2379G>A		intron_variant			NM_004093.4	P1
	ENST00000646480.1	n.497-942C>T		intron_variant, non_coding_transcript_variant
EFNB2	ENST00000643990.1	n.10+1247G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81139 AN: 151866 Hom.: 22750 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.534 AC: 81182 AN: 151984 Hom.: 22763 Cov.: 32 AF XY: 0.538 AC XY: 39962 AN XY: 74258

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.525

Alfa AF: 0.586 Hom.: 53989

Bravo AF: 0.515

Asia WGS AF: 0.589 AC: 2047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.030
Dann	Benign	0.78

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: rs9520092; hg19: chr13-107167539;