rs11543
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001391963.1(VDAC2):c.-109G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 328,884 control chromosomes in the GnomAD database, including 72,903 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 0.69 ( 38630 hom., cov: 33)
Exomes 𝑓: 0.60 ( 34273 hom. )
Consequence
VDAC2
NM_001391963.1 5_prime_UTR
NM_001391963.1 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.529
Genes affected
VDAC2 (HGNC:12672): (voltage dependent anion channel 2) This gene encodes a member of the voltage-dependent anion channel pore-forming family of proteins that are considered the main pathway for metabolite diffusion across the mitochondrial outer membrane. The encoded protein is also thought to be involved in the mitochondrial apoptotic pathway via regulation of BCL2-antagonist/killer 1 protein activity. Pseudogenes have been identified on chromosomes 1, 2, 12 and 21, and alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
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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=-0.76).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VDAC2 | NM_001391963.1 | c.-109G>C | 5_prime_UTR_variant | 1/10 | ENST00000332211.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VDAC2 | ENST00000332211.11 | c.-109G>C | 5_prime_UTR_variant | 1/10 | 1 | NM_001391963.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.690 AC: 104877AN: 151946Hom.: 38567 Cov.: 33
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GnomAD4 exome AF: 0.604 AC: 106780AN: 176820Hom.: 34273 Cov.: 2 AF XY: 0.603 AC XY: 54768AN XY: 90876
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GnomAD4 genome ? AF: 0.690 AC: 104996AN: 152064Hom.: 38630 Cov.: 33 AF XY: 0.695 AC XY: 51651AN XY: 74338
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at