Variant rs688969 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFNB1	NM_004429.5 linkuse as main transcript	c.*734A>C		3_prime_UTR_variant	5/5	ENST00000204961.5	NP_004420.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFNB1	ENST00000204961.5 linkuse as main transcript	c.*734A>C		3_prime_UTR_variant	5/5	1	NM_004429.5	ENSP00000204961	P1

Frequencies

GnomAD3 genomes

AF:

0.610

AC:

66121

AN:

108461

Hom.:

15201

Cov.:

AF XY:

0.580

AC XY:

18091

AN XY:

31217

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

Gnomad4 AFR exome

AF:

1.00

Gnomad4 AMR exome

AF:

1.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.750

Gnomad4 FIN exome

AF:

0.560

Gnomad4 NFE exome

AF:

0.821

Gnomad4 OTH exome

AF:

0.667

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

Gnomad4 AFR

AF:

0.731

Gnomad4 AMR

AF:

0.548

Gnomad4 ASJ

AF:

0.545

Gnomad4 EAS

AF:

0.369

Gnomad4 SAS

AF:

0.399

Gnomad4 FIN

AF:

0.521

Gnomad4 NFE

AF:

0.592

Gnomad4 OTH

AF:

0.617

Alfa

AF:

0.562

Hom.:

3176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.0

DANN

Benign

0.47

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over