dbSNP rs688969: EFNB1:c.*734A>C (chrX-68841388-A-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_004429.5(EFNB1):c.*734A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.61 ( 15197 hom., 18119 hem., cov: 22)

Exomes 𝑓: 0.61 ( 40 hom. 99 hem. )

Failed GnomAD Quality Control

Consequence

EFNB1
NM_004429.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.470

Publications

3 publications found

Variant links:

Genes affected

EFNB1 (HGNC:3226): (ephrin B1) The protein encoded by this gene is a type I membrane protein and a ligand of Eph-related receptor tyrosine kinases. It may play a role in cell adhesion and function in the development or maintenance of the nervous system. [provided by RefSeq, Jul 2008]

EFNB1 Gene-Disease associations (from GenCC):

craniofrontonasal syndrome
Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, G2P, Genomics England PanelApp, ClinGen, Labcorp Genetics (formerly Invitae)

EFNB1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_004429.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004429.5. 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
	EFNB1	NM_004429.5	MANE Select	c.*734A>C		3_prime_UTR	Exon 5 of 5	NP_004420.1	P98172

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFNB1	ENST00000204961.5	TSL:1 MANE Select	c.*734A>C		3_prime_UTR	Exon 5 of 5	ENSP00000204961.4	P98172
	EFNB1	ENST00000851101.1		c.*734A>C		3_prime_UTR	Exon 4 of 4	ENSP00000521160.1

Frequencies

GnomAD3 genomes

AF:

0.610

AC:

66121

AN:

108461

Hom.:

15201

Cov.:

show subpopulations

Gnomad AFR

AF:

0.732

Gnomad AMI

AF:

0.573

Gnomad AMR

AF:

0.547

Gnomad ASJ

AF:

0.545

Gnomad EAS

AF:

0.369

Gnomad SAS

AF:

0.400

Gnomad FIN

AF:

0.521

Gnomad MID

AF:

0.634

Gnomad NFE

AF:

0.592

Gnomad OTH

AF:

0.624

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.610

AC:

225

AN:

369

Hom.:

Cov.:

AF XY:

0.631

AC XY:

AN XY:

157

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

0.560

AC:

163

AN:

291

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.821

AC:

AN:

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

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

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.610

AC:

66140

AN:

108506

Hom.:

15197

Cov.:

AF XY:

0.579

AC XY:

18119

AN XY:

31274

show subpopulations

African (AFR)

AF:

0.731

AC:

21591

AN:

29518

American (AMR)

AF:

0.548

AC:

5685

AN:

10378

Ashkenazi Jewish (ASJ)

AF:

0.545

AC:

1416

AN:

2598

East Asian (EAS)

AF:

0.369

AC:

1245

AN:

3377

South Asian (SAS)

AF:

0.399

AC:

1032

AN:

2585

European-Finnish (FIN)

AF:

0.521

AC:

2876

AN:

5522

Middle Eastern (MID)

AF:

0.612

AC:

126

AN:

206

European-Non Finnish (NFE)

AF:

0.592

AC:

30881

AN:

52188

Other (OTH)

AF:

0.617

AC:

912

AN:

1478

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

896

1792

2687

3583

4479

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

568

1136

1704

2272

2840

<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:

0.562

Hom.:

3176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.0

(source)

DANN

Benign

0.47

PhyloP100

0.47

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over