rs11568820

chr12-47908762-C-T

Variant summary

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

The ENST00000395324.6(VDR):c.-83-25988G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,090 control chromosomes in the GnomAD database, including 16,359 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 0.38 (16359 hom., cov: 31)
• Consequence: VDR ENST00000395324.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

VDR (HGNC:12679): (vitamin D receptor) This gene encodes vitamin D3 receptor, which is a member of the nuclear hormone receptor superfamily of ligand-inducible transcription factors. This receptor also functions as a receptor for the secondary bile acid, lithocholic acid. Downstream targets of vitamin D3 receptor are principally involved in mineral metabolism, though this receptor regulates a variety of other metabolic pathways, such as those involved in immune response and cancer. Mutations in this gene are associated with type II vitamin D-resistant rickets. A single nucleotide polymorphism in the initiation codon results in an alternate translation start site three codons downstream. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. A recent study provided evidence for translational readthrough in this gene, and expression of an additional C-terminally extended isoform via the use of an alternative in-frame translation termination codon. [provided by RefSeq, Jun 2018]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VDR	ENST00000395324.6	c.-83-25988G>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57431 AN: 151972 Hom.: 16322 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.378 AC: 57511 AN: 152090 Hom.: 16359 Cov.: 31 AF XY: 0.373 AC XY: 27764 AN XY: 74342

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.351

Alfa AF: 0.281 Hom.: 3191

Bravo AF: 0.403

Asia WGS AF: 0.386 AC: 1341 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.92
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11568820; hg19: chr12-48302545;