chr13-106510512-A-G

Variant names:

• chr13-106510512-A-G
• rs7327929
• NM_004093.4:c.406+2017T>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.406+2017T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,158 control chromosomes in the GnomAD database, including 19,655 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 0.50 (19655 hom., cov: 33)
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFNB2	NM_004093.4	c.406+2017T>C		intron_variant	Intron 2 of 4	ENST00000646441.1	NP_004084.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFNB2	ENST00000646441.1	c.406+2017T>C		intron_variant	Intron 2 of 4		NM_004093.4	ENSP00000493716.1
EFNB2	ENST00000643990.1	n.10+5926T>C		intron_variant	Intron 1 of 3
ENSG00000284966	ENST00000646480.1	n.497-5621A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75282 AN: 152040 Hom.: 19646 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.495 AC: 75330 AN: 152158 Hom.: 19655 Cov.: 33 AF XY: 0.501 AC XY: 37273 AN XY: 74374

African (AFR) AF: 0.330 AC: 13718 AN: 41510

American (AMR) AF: 0.506 AC: 7736 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1535 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3075 AN: 5154

South Asian (SAS) AF: 0.498 AC: 2400 AN: 4822

European-Finnish (FIN) AF: 0.628 AC: 6654 AN: 10588

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38466 AN: 67998

Other (OTH) AF: 0.500 AC: 1056 AN: 2114

Alfa AF: 0.533 Hom.: 4536

Bravo AF: 0.476

Asia WGS AF: 0.542 AC: 1881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.075
DANN	Benign	0.54
PhyloP100		-1.7
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: rs7327929; hg19: chr13-107162860;