rs30499

Positions:

• chr5-134106035-C-T

Variant summary

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

The NM_001401009.1(VDAC1):​c.-327G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,156 control chromosomes in the GnomAD database, including 35,354 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 0.67 (35354 hom., cov: 33)
• Consequence: VDAC1 NM_001401009.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

Genes affected

VDAC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VDAC1	NM_001401009.1	c.-327G>A		5_prime_UTR_variant	1/10		NP_001387938.1
VDAC1	NM_001401010.1	c.-453G>A		5_prime_UTR_variant	1/11		NP_001387939.1
VDAC1	NM_001401011.1	c.-598G>A		5_prime_UTR_variant	1/12		NP_001387940.1
VDAC1	NM_001401008.1	c.-174-405G>A		intron_variant			NP_001387937.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102251 AN: 152038 Hom.: 35348 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.672 AC: 102296 AN: 152156 Hom.: 35354 Cov.: 33 AF XY: 0.664 AC XY: 49396 AN XY: 74412

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.686

Alfa AF: 0.741 Hom.: 56134

Bravo AF: 0.660

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.83
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30499; hg19: chr5-133441726;