chr10-75212086-C-G

Variant names:

• chr10-75212086-C-G
• rs2804535
• NM_001391963.1:c.32-144C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001391963.1(VDAC2):​c.32-144C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: VDAC2 NM_001391963.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VDAC2	NM_001391963.1	c.32-144C>G		intron_variant	Intron 2 of 9	ENST00000332211.11	NP_001378892.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VDAC2	ENST00000332211.11	c.32-144C>G		intron_variant	Intron 2 of 9	1	NM_001391963.1	ENSP00000361686.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 550438 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 293762

African (AFR) AF: 0.00 AC: 0 AN: 13804

American (AMR) AF: 0.00 AC: 0 AN: 20412

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18042

East Asian (EAS) AF: 0.00 AC: 0 AN: 31488

South Asian (SAS) AF: 0.00 AC: 0 AN: 54596

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36604

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3038

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 342864

Other (OTH) AF: 0.00 AC: 0 AN: 29590

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.48
PhyloP100		0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2804535; hg19: chr10-76971844;