rs3025039

Variant summary

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

The NM_003376(VEGFA):c.*237C>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 0.129 in 151728 control chromosomes in the gnomAD Genomes database, including 1462 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as other (no stars).

Frequency

Genomes: 𝑓 0.13 ( 1462 hom., cov: 31)

Consequence

VEGFA
NM_003376 3_prime_UTR

Scores

Clinical Significance

other no assertion criteria provided O:1

Conservation

PhyloP100: 0.0550

Links

VEGFA (HGNC:12680):

POLR1C (HGNC:):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BA1

GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VEGFA	NM_003376.6 linkuse as main transcript	c.*237C>T		3_prime_UTR_variant	8/8	ENST00000672860.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VEGFA	ENST00000672860.3 linkuse as main transcript	c.*237C>T		3_prime_UTR_variant	8/8		NM_003376.6		P15692-13

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19602

AN:

151728

Hom.:

1462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0849

Gnomad AMI

AF:

0.0802

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.175

Gnomad SAS

AF:

0.0972

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.127

GnomAD4 exome

AF:

0.146

AC:

80486

AN:

550102

Hom.:

6449

AF XY:

0.143

AC XY:

41724

AN XY:

292778

show subpopulations

Gnomad4 AFR exome

AF:

0.0853

Gnomad4 AMR exome

AF:

0.270

Gnomad4 ASJ exome

AF:

0.135

Gnomad4 EAS exome

AF:

0.196

Gnomad4 SAS exome

AF:

0.0975

Gnomad4 FIN exome

AF:

0.149

Gnomad4 NFE exome

AF:

0.142

Gnomad4 OTH exome

AF:

0.138

Alfa

AF:

0.141

Hom.:

1927

Bravo

AF:

0.134

Asia WGS

AF:

0.138

AC:

481

AN:

3478

ClinVar

Significance: other

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Cholangiocarcinoma

Other:1

other, no assertion criteria provided

research

Department of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin Berlin

Dec 10, 2022

No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

Cadd

Benign

Dann

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over