rs30503

chr5-134101655-G-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+3808C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,020 control chromosomes in the GnomAD database, including 5,963 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 0.24 (5963 hom., cov: 31)
• Consequence: VDAC1 NM_001401008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631

Genes affected

VDAC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VDAC1	NM_001401008.1	c.-7+3808C>G		intron_variant
VDAC1	NM_001401009.1	c.-4+3808C>G		intron_variant
VDAC1	NM_001401010.1	c.-130+3808C>G		intron_variant
VDAC1	NM_001401011.1	c.-275+3808C>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36671 AN: 151904 Hom.: 5952 Cov.: 31

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.242 AC: 36729 AN: 152020 Hom.: 5963 Cov.: 31 AF XY: 0.247 AC XY: 18319 AN XY: 74296

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.218

Alfa AF: 0.180 Hom.: 456

Bravo AF: 0.264

Asia WGS AF: 0.262 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.1
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30503; hg19: chr5-133437346;