rs2391337

Variant names:

• chr13-106521008-G-A
• rs2391337
• NM_004093.4:c.123-8196C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-106521008-G-A
• chr13-106521008-G-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.123-8196C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,110 control chromosomes in the GnomAD database, including 50,245 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 0.81 (50245 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744
• Publications: 0 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 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.123-8196C>T		intron	N/A	NP_004084.1	P52799
	EFNB2	NM_001372056.1		c.123-8196C>T		intron	N/A	NP_001358985.1
	EFNB2	NM_001372057.1		c.123-8196C>T		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.123-8196C>T		intron	N/A	ENSP00000493716.1	P52799
	EFNB2	ENST00000955444.1		c.123-8196C>T		intron	N/A	ENSP00000625503.1
	ENSG00000284966	ENST00000646480.1		n.5372G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123364 AN: 151992 Hom.: 50213 Cov.: 31

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.812

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.812 AC: 123454 AN: 152110 Hom.: 50245 Cov.: 31 AF XY: 0.813 AC XY: 60457 AN XY: 74344

African (AFR) AF: 0.752 AC: 31193 AN: 41470

American (AMR) AF: 0.800 AC: 12234 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2825 AN: 3472

East Asian (EAS) AF: 0.877 AC: 4543 AN: 5180

South Asian (SAS) AF: 0.808 AC: 3884 AN: 4808

European-Finnish (FIN) AF: 0.850 AC: 9005 AN: 10598

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.839 AC: 57012 AN: 67982

Other (OTH) AF: 0.810 AC: 1711 AN: 2112

Alfa AF: 0.831 Hom.: 67037

Bravo AF: 0.806

Asia WGS AF: 0.829 AC: 2886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		0.74
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: rs2391337; hg19: chr13-107173356;