rs2010963
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003376(VEGFA):c.-94C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151946 control chromosomes in the gnomAD Genomes database, including 35315 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.68 ( 35315 hom., cov: 33)
Consequence
VEGFA
NM_003376 5_prime_UTR
NM_003376 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.03
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 6:43770613-C>G is Benign according to our data. Variant chr6-43770613-C-G is described in ClinVar as [Benign]. Clinvar id is 12223. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VEGFA | NM_003376.6 | c.-94C>G | 5_prime_UTR_variant | 1/8 | ENST00000672860.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VEGFA | ENST00000672860.3 | c.-94C>G | 5_prime_UTR_variant | 1/8 | NM_003376.6 | ||||
ENST00000607600.1 | n.4G>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.682 AC: 103572AN: 151946Hom.: 35315 Cov.: 33
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GnomAD4 exome AF: 0.684 AC: 886758AN: 1297288Hom.: 304109 AF XY: 0.684 AC XY: 436658AN XY: 638118
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ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | This variant is associated with the following publications: (PMID: 27648002, 25992764, 23957473, 25328912, 22993299, 15338501, 11978667, 24205329, 23007030, 16142870, 19653005, 23353010, 10930302, 15963467) - |
Microvascular complications of diabetes, susceptibility to, 1 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | May 01, 2002 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at