13-106515142-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004093.4(EFNB2):​c.123-2330C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,130 control chromosomes in the GnomAD database, including 51,284 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 ( 51284 hom., cov: 32)

Consequence

EFNB2
NM_004093.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.520
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EFNB2NM_004093.4 linkc.123-2330C>A intron_variant Intron 1 of 4 ENST00000646441.1 NP_004084.1 P52799

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EFNB2ENST00000646441.1 linkc.123-2330C>A intron_variant Intron 1 of 4 NM_004093.4 ENSP00000493716.1 P52799
EFNB2ENST00000643990.1 linkn.10+1296C>A intron_variant Intron 1 of 3
ENSG00000284966ENST00000646480.1 linkn.497-991G>T intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.810
AC:
123196
AN:
152012
Hom.:
51259
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.608
Gnomad AMI
AF:
0.966
Gnomad AMR
AF:
0.809
Gnomad ASJ
AF:
0.934
Gnomad EAS
AF:
0.759
Gnomad SAS
AF:
0.874
Gnomad FIN
AF:
0.931
Gnomad MID
AF:
0.911
Gnomad NFE
AF:
0.904
Gnomad OTH
AF:
0.847
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.810
AC:
123267
AN:
152130
Hom.:
51284
Cov.:
32
AF XY:
0.814
AC XY:
60501
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.609
Gnomad4 AMR
AF:
0.809
Gnomad4 ASJ
AF:
0.934
Gnomad4 EAS
AF:
0.759
Gnomad4 SAS
AF:
0.875
Gnomad4 FIN
AF:
0.931
Gnomad4 NFE
AF:
0.904
Gnomad4 OTH
AF:
0.847
Alfa
AF:
0.880
Hom.:
10116
Bravo
AF:
0.788
Asia WGS
AF:
0.806
AC:
2804
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.76
DANN
Benign
0.70

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9520091; hg19: chr13-107167490; API