Genetic Variant EFNB2:c.*1068C>T (chr13-106491972-G-A) – 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.*1068C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,416 control chromosomes in the GnomAD database, including 18,656 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 0.49 ( 18621 hom., cov: 32)

Exomes 𝑓: 0.40 ( 35 hom. )

Consequence

EFNB2
NM_004093.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32

Publications

17 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
EFNB2	NM_004093.4 link	c.*1068C>T	3_prime_UTR_variant	Exon 5 of 5	ENST00000646441.1	NP_004084.1	P52799
EFNB2	NM_001372056.1 link	c.*1068C>T	3_prime_UTR_variant	Exon 4 of 4		NP_001358985.1
EFNB2	NM_001372057.1 link	c.*1068C>T	3_prime_UTR_variant	Exon 4 of 4		NP_001358986.1
EFNB2	XM_017020406.3 link	c.*1068C>T	3_prime_UTR_variant	Exon 5 of 5		XP_016875895.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
EFNB2	ENST00000646441.1 link	c.*1068C>T	3_prime_UTR_variant	Exon 5 of 5	NM_004093.4	ENSP00000493716.1	P52799
EFNB2	ENST00000643990.1 link	n.1674C>T	non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000284966	ENST00000649449.1 link	n.559+267G>A	intron_variant	Intron 1 of 3
ENSG00000284966	ENST00000646480.1 link	n.-176G>A	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.488

AC:

74092

AN:

151838

Hom.:

18580

Cov.:

show subpopulations

Gnomad AFR

AF:

0.591

Gnomad AMI

AF:

0.488

Gnomad AMR

AF:

0.482

Gnomad ASJ

AF:

0.450

Gnomad EAS

AF:

0.626

Gnomad SAS

AF:

0.574

Gnomad FIN

AF:

0.393

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.426

Gnomad OTH

AF:

0.512

GnomAD4 exome

AF:

0.396

AC:

182

AN:

460

Hom.:

Cov.:

AF XY:

0.397

AC XY:

112

AN XY:

282

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.386

AC:

166

AN:

430

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.488

AC:

74191

AN:

151956

Hom.:

18621

Cov.:

AF XY:

0.487

AC XY:

36185

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.592

AC:

24521

AN:

41440

American (AMR)

AF:

0.482

AC:

7366

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.450

AC:

1560

AN:

3466

East Asian (EAS)

AF:

0.625

AC:

3227

AN:

5162

South Asian (SAS)

AF:

0.574

AC:

2763

AN:

4816

European-Finnish (FIN)

AF:

0.393

AC:

4137

AN:

10534

Middle Eastern (MID)

AF:

0.449

AC:

132

AN:

294

European-Non Finnish (NFE)

AF:

0.426

AC:

28955

AN:

67948

Other (OTH)

AF:

0.515

AC:

1086

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1898

3795

5693

7590

9488

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

670

1340

2010

2680

3350

<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:

0.461

Hom.:

44263

Bravo

AF:

0.502

Asia WGS

AF:

0.615

AC:

2142

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

0.074

(source)

DANN

Benign

0.76

PhyloP100

-1.3

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