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GeneBe

rs7970314

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000395324.6(VDR):c.-84+28472T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,102 control chromosomes in the GnomAD database, including 18,413 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 0.41 ( 18413 hom., cov: 31)

Consequence

VDR
ENST00000395324.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.45
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 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
VDRENST00000395324.6 linkuse as main transcriptc.-84+28472T>C intron_variant 5 P1P11473-1

Frequencies

GnomAD3 genomes
AF:
0.405
AC:
61604
AN:
151984
Hom.:
18366
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.833
Gnomad AMI
AF:
0.172
Gnomad AMR
AF:
0.254
Gnomad ASJ
AF:
0.287
Gnomad EAS
AF:
0.553
Gnomad SAS
AF:
0.414
Gnomad FIN
AF:
0.169
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.214
Gnomad OTH
AF:
0.382
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.406
AC:
61691
AN:
152102
Hom.:
18413
Cov.:
31
AF XY:
0.403
AC XY:
29940
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.833
Gnomad4 AMR
AF:
0.254
Gnomad4 ASJ
AF:
0.287
Gnomad4 EAS
AF:
0.552
Gnomad4 SAS
AF:
0.413
Gnomad4 FIN
AF:
0.169
Gnomad4 NFE
AF:
0.214
Gnomad4 OTH
AF:
0.378
Alfa
AF:
0.254
Hom.:
10748
Bravo
AF:
0.430
Asia WGS
AF:
0.468
AC:
1628
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.27
Dann
Benign
0.42

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7970314; hg19: chr12-48308174; API