10-75222255-T-C
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001391963.1(VDAC2):āc.588T>Cā(p.Asn196=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00336 in 1,613,458 control chromosomes in the GnomAD database, including 153 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.018 ( 89 hom., cov: 33)
Exomes š: 0.0018 ( 64 hom. )
Consequence
VDAC2
NM_001391963.1 synonymous
NM_001391963.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.01
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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 10-75222255-T-C is Benign according to our data. Variant chr10-75222255-T-C is described in ClinVar as [Benign]. Clinvar id is 786166.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.01 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0594 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VDAC2 | NM_001391963.1 | c.588T>C | p.Asn196= | synonymous_variant | 8/10 | ENST00000332211.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VDAC2 | ENST00000332211.11 | c.588T>C | p.Asn196= | synonymous_variant | 8/10 | 1 | NM_001391963.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0179 AC: 2719AN: 152210Hom.: 89 Cov.: 33
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GnomAD3 exomes AF: 0.00492 AC: 1235AN: 250964Hom.: 32 AF XY: 0.00357 AC XY: 484AN XY: 135660
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GnomAD4 exome AF: 0.00184 AC: 2695AN: 1461130Hom.: 64 Cov.: 31 AF XY: 0.00161 AC XY: 1172AN XY: 726872
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GnomAD4 genome AF: 0.0179 AC: 2720AN: 152328Hom.: 89 Cov.: 33 AF XY: 0.0170 AC XY: 1265AN XY: 74500
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 21, 2018 | - - |
Computational scores
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Benign
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DANN
Benign
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RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at