chr13-106508560-T-C

Variant names:

• chr13-106508560-T-C
• rs8002701
• NM_004093.4:c.406+3969A>G

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+3969A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,890 control chromosomes in the GnomAD database, including 22,645 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 0.54 (22645 hom., cov: 31)
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 2 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=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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.406+3969A>G		intron	N/A	NP_004084.1	P52799
	EFNB2	NM_001372056.1		c.406+3969A>G		intron	N/A	NP_001358985.1
	EFNB2	NM_001372057.1		c.406+3969A>G		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.406+3969A>G		intron	N/A	ENSP00000493716.1	P52799
	EFNB2	ENST00000955444.1		c.406+3969A>G		intron	N/A	ENSP00000625503.1
	ENSG00000284966	ENST00000642447.1		n.86-1259T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82418 AN: 151772 Hom.: 22609 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.543 AC: 82506 AN: 151890 Hom.: 22645 Cov.: 31 AF XY: 0.545 AC XY: 40472 AN XY: 74206

African (AFR) AF: 0.499 AC: 20665 AN: 41414

American (AMR) AF: 0.522 AC: 7968 AN: 15272

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

East Asian (EAS) AF: 0.568 AC: 2923 AN: 5142

South Asian (SAS) AF: 0.505 AC: 2432 AN: 4820

European-Finnish (FIN) AF: 0.629 AC: 6622 AN: 10532

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38560 AN: 67930

Other (OTH) AF: 0.528 AC: 1114 AN: 2110

Alfa AF: 0.547 Hom.: 25114

Bravo AF: 0.531

Asia WGS AF: 0.544 AC: 1889 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	17
DANN	Benign	0.81
PhyloP100		0.33
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: rs8002701; hg19: chr13-107160908;