rs7304
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_001391963.1(VDAC2):c.*218A>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0395 in 454,128 control chromosomes in the GnomAD database, including 585 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 0.054 ( 350 hom., cov: 33)
Exomes 𝑓: 0.032 ( 235 hom. )
Consequence
VDAC2
NM_001391963.1 3_prime_UTR
NM_001391963.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.21
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VDAC2 | NM_001391963.1 | c.*218A>G | 3_prime_UTR_variant | 10/10 | ENST00000332211.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VDAC2 | ENST00000332211.11 | c.*218A>G | 3_prime_UTR_variant | 10/10 | 1 | NM_001391963.1 | P1 | ||
VDAC2 | ENST00000313132.8 | c.*218A>G | 3_prime_UTR_variant | 11/11 | 1 | ||||
VDAC2 | ENST00000543351.5 | c.*218A>G | 3_prime_UTR_variant | 10/10 | 5 | P1 | |||
VDAC2 | ENST00000460044.1 | n.702A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0536 AC: 8155AN: 152150Hom.: 352 Cov.: 33
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GnomAD4 exome AF: 0.0324 AC: 9778AN: 301860Hom.: 235 Cov.: 3 AF XY: 0.0341 AC XY: 5354AN XY: 157210
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GnomAD4 genome ? AF: 0.0536 AC: 8155AN: 152268Hom.: 350 Cov.: 33 AF XY: 0.0524 AC XY: 3905AN XY: 74460
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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