dbSNP rs3742160: EFNB2:c.614-53T>A (chr13-106493481-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004093.4(EFNB2):c.614-53T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 1,548,130 control chromosomes in the GnomAD database, including 65,184 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 0.31 ( 7696 hom., cov: 32)

Exomes 𝑓: 0.28 ( 57488 hom. )

Consequence

EFNB2
NM_004093.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.149

Publications

8 publications found

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]

EFNB2 links:

ENSG00000284966 (HGNC:):

ENSG00000284966 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
EFNB2	NM_004093.4 link	c.614-53T>A	intron_variant	Intron 4 of 4	ENST00000646441.1	NP_004084.1	P52799
EFNB2	NM_001372056.1 link	c.521-53T>A	intron_variant	Intron 3 of 3		NP_001358985.1
EFNB2	NM_001372057.1 link	c.500-53T>A	intron_variant	Intron 3 of 3		NP_001358986.1
EFNB2	XM_017020406.3 link	c.620-53T>A	intron_variant	Intron 4 of 4		XP_016875895.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFNB2	ENST00000646441.1 link	c.614-53T>A		intron_variant	Intron 4 of 4		NM_004093.4	ENSP00000493716.1		P52799

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47351

AN:

151976

Hom.:

7673

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.385

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.423

Gnomad SAS

AF:

0.409

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.259

Gnomad OTH

AF:

0.339

GnomAD4 exome

AF:

0.281

AC:

392486

AN:

1396036

Hom.:

57488

AF XY:

0.284

AC XY:

195096

AN XY:

686800

show subpopulations

African (AFR)

AF:

0.379

AC:

11986

AN:

31652

American (AMR)

AF:

0.421

AC:

15869

AN:

37714

Ashkenazi Jewish (ASJ)

AF:

0.327

AC:

7173

AN:

21904

East Asian (EAS)

AF:

0.441

AC:

17192

AN:

39026

South Asian (SAS)

AF:

0.394

AC:

30445

AN:

77346

European-Finnish (FIN)

AF:

0.220

AC:

10220

AN:

46520

Middle Eastern (MID)

AF:

0.371

AC:

2023

AN:

5446

European-Non Finnish (NFE)

AF:

0.260

AC:

280145

AN:

1078886

Other (OTH)

AF:

0.303

AC:

17433

AN:

57542

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

15198

30396

45594

60792

75990

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10020

20040

30060

40080

50100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.312

AC:

47414

AN:

152094

Hom.:

7696

Cov.:

AF XY:

0.313

AC XY:

23265

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.376

AC:

15594

AN:

41456

American (AMR)

AF:

0.360

AC:

5505

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.313

AC:

1086

AN:

3470

East Asian (EAS)

AF:

0.424

AC:

2184

AN:

5156

South Asian (SAS)

AF:

0.408

AC:

1964

AN:

4812

European-Finnish (FIN)

AF:

0.216

AC:

2288

AN:

10594

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.259

AC:

17618

AN:

67992

Other (OTH)

AF:

0.337

AC:

712

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1672

3344

5016

6688

8360

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.282

Hom.:

799

Bravo

AF:

0.327

Asia WGS

AF:

0.395

AC:

1378

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.12

(source)

DANN

Benign

0.55

PhyloP100

-0.15

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over