Variant chr11-64236371-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003377.5(VEGFB):c.374+44G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,591,162 control chromosomes in the GnomAD database, including 89,761 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 0.28 ( 6646 hom., cov: 31)

Exomes 𝑓: 0.34 ( 83115 hom. )

Consequence

VEGFB
NM_003377.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.452

Variant links:

Genes affected

VEGFB (HGNC:12681): (vascular endothelial growth factor B) This gene encodes a member of the PDGF (platelet-derived growth factor)/VEGF (vascular endothelial growth factor) family. The VEGF family members regulate the formation of blood vessels and are involved in endothelial cell physiology. This member is a ligand for VEGFR-1 (vascular endothelial growth factor receptor 1) and NRP-1 (neuropilin-1). Studies in mice showed that this gene was co-expressed with nuclear-encoded mitochondrial genes and the encoded protein specifically controlled endothelial uptake of fatty acids. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Sep 2011]

VEGFB links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VEGFB	NM_003377.5 linkuse as main transcript	c.374+44G>T		intron_variant		ENST00000309422.7	NP_003368.1	P49765-1Q7LAP4
VEGFB	NM_001243733.2 linkuse as main transcript	c.374+44G>T		intron_variant			NP_001230662.1	P49765-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VEGFB	ENST00000309422.7 linkuse as main transcript	c.374+44G>T		intron_variant		1	NM_003377.5	ENSP00000311127.2		P49765-1
VEGFB	ENST00000426086.3 linkuse as main transcript	c.374+44G>T		intron_variant		1		ENSP00000401550.2		P49765-2

Frequencies

GnomAD3 genomes

AF:

0.283

AC:

42960

AN:

151860

Hom.:

6642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.280

Gnomad AMR

AF:

0.372

Gnomad ASJ

AF:

0.242

Gnomad EAS

AF:

0.273

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.303

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.301

GnomAD3 exomes

AF:

0.306

AC:

74868

AN:

244836

Hom.:

12088

AF XY:

0.303

AC XY:

40209

AN XY:

132816

show subpopulations

Gnomad AFR exome

AF:

0.152

Gnomad AMR exome

AF:

0.394

Gnomad ASJ exome

AF:

0.243

Gnomad EAS exome

AF:

0.271

Gnomad SAS exome

AF:

0.187

Gnomad FIN exome

AF:

0.315

Gnomad NFE exome

AF:

0.342

Gnomad OTH exome

AF:

0.320

GnomAD4 exome

AF:

0.335

AC:

482629

AN:

1439186

Hom.:

83115

Cov.:

AF XY:

0.331

AC XY:

237258

AN XY:

716912

show subpopulations

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.399

Gnomad4 ASJ exome

AF:

0.240

Gnomad4 EAS exome

AF:

0.290

Gnomad4 SAS exome

AF:

0.186

Gnomad4 FIN exome

AF:

0.316

Gnomad4 NFE exome

AF:

0.356

Gnomad4 OTH exome

AF:

0.321

GnomAD4 genome

AF:

0.283

AC:

42983

AN:

151976

Hom.:

6646

Cov.:

AF XY:

0.282

AC XY:

20933

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.155

Gnomad4 AMR

AF:

0.372

Gnomad4 ASJ

AF:

0.242

Gnomad4 EAS

AF:

0.272

Gnomad4 SAS

AF:

0.179

Gnomad4 FIN

AF:

0.303

Gnomad4 NFE

AF:

0.347

Gnomad4 OTH

AF:

0.305

Alfa

AF:

0.319

Hom.:

7540

Bravo

AF:

0.285

Asia WGS

AF:

0.243

AC:

844

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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