13-106527626-T-G

Variant names:

• chr13-106527626-T-G
• rs8000078
• NM_004093.4:c.122+7217A>C

Variant summary

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

The NM_004093.4(EFNB2):​c.122+7217A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,102 control chromosomes in the GnomAD database, including 27,562 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 0.60 (27562 hom., cov: 33)
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFNB2	NM_004093.4	c.122+7217A>C		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.122+7217A>C		intron_variant	Intron 1 of 4		NM_004093.4	ENSP00000493716.1

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90742 AN: 151984 Hom.: 27520 Cov.: 33

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.597 AC: 90843 AN: 152102 Hom.: 27562 Cov.: 33 AF XY: 0.599 AC XY: 44559 AN XY: 74330

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.593

Alfa AF: 0.546 Hom.: 45177

Bravo AF: 0.607

Asia WGS AF: 0.703 AC: 2442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.6
DANN	Benign	0.77

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: rs8000078; hg19: chr13-107179974;