chr13-106527626-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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.122+7217A>C		intron	N/A	NP_004084.1	P52799
	EFNB2	NM_001372056.1		c.122+7217A>C		intron	N/A	NP_001358985.1
	EFNB2	NM_001372057.1		c.122+7217A>C		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.122+7217A>C		intron	N/A	ENSP00000493716.1	P52799
	EFNB2	ENST00000955444.1		c.122+7217A>C		intron	N/A	ENSP00000625503.1

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

African (AFR) AF: 0.651 AC: 27035 AN: 41504

American (AMR) AF: 0.652 AC: 9969 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1691 AN: 3466

East Asian (EAS) AF: 0.825 AC: 4263 AN: 5166

South Asian (SAS) AF: 0.622 AC: 2996 AN: 4818

European-Finnish (FIN) AF: 0.582 AC: 6151 AN: 10566

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36797 AN: 67982

Other (OTH) AF: 0.593 AC: 1249 AN: 2108

Alfa AF: 0.557 Hom.: 73235

Bravo AF: 0.607

Asia WGS AF: 0.703 AC: 2442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.6
DANN	Benign	0.77
PhyloP100		-0.11
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: rs8000078; hg19: chr13-107179974;