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
NM_003376 3_prime_UTR
Scores
2
Clinical Significance
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 |
---|---|---|---|---|---|---|---|
VEGFA | NM_003376.6 | 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 | c.*237C>T | 3_prime_UTR_variant | 8/8 | NM_003376.6 |
Frequencies
GnomAD3 genomes AF: 0.129 AC: 19602AN: 151728Hom.: 1462 Cov.: 31
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GnomAD4 exome AF: 0.146 AC: 80486AN: 550102Hom.: 6449 AF XY: 0.143 AC XY: 41724AN XY: 292778
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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
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at