rs30500

chr5-134104185-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001401008.1(VDAC1):c.-7+1278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,166 control chromosomes in the GnomAD database, including 44,502 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 0.76 (44502 hom., cov: 33)
• Consequence: VDAC1 NM_001401008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902

Genes affected

VDAC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VDAC1	NM_001401008.1	c.-7+1278A>G		intron_variant
VDAC1	NM_001401009.1	c.-4+1278A>G		intron_variant
VDAC1	NM_001401010.1	c.-130+1278A>G		intron_variant
VDAC1	NM_001401011.1	c.-275+1278A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115576 AN: 152048 Hom.: 44471 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.781

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.760 AC: 115666 AN: 152166 Hom.: 44502 Cov.: 33 AF XY: 0.757 AC XY: 56349 AN XY: 74398

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.782

Alfa AF: 0.805 Hom.: 61387

Bravo AF: 0.751

Asia WGS AF: 0.648 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	11
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30500; hg19: chr5-133439876;