Menu
GeneBe

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: đť‘“ 0.13 ( 1462 hom., cov: 31)

Consequence

VEGFA
NM_003376 3_prime_UTR

Scores

2

Clinical Significance

other no assertion criteria provided O:1

Conservation

PhyloP100: 0.0550

Links

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
VEGFANM_003376.6 linkuse as main transcriptc.*237C>T 3_prime_UTR_variant 8/8 ENST00000672860.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
VEGFAENST00000672860.3 linkuse as main transcriptc.*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.:
31
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 providedresearchDepartment of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin BerlinDec 10, 2022No 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
16
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.

Other links and lift over

dbSNP: rs3025039; hg19: chr6-43752536; COSMIC: COSV57878013; COSMIC: COSV57878013;