12-47846052-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000376.3(VDR):c.1024+283G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,108 control chromosomes in the GnomAD database, including 9,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.35 ( 9698 hom., cov: 32)
Consequence
VDR
NM_000376.3 intron
NM_000376.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0330
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 12-47846052-C-T is Benign according to our data. Variant chr12-47846052-C-T is described in ClinVar as [Benign]. Clinvar id is 1259287.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VDR | NM_000376.3 | c.1024+283G>A | intron_variant | ENST00000549336.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VDR | ENST00000549336.6 | c.1024+283G>A | intron_variant | 1 | NM_000376.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.349 AC: 52971AN: 151990Hom.: 9691 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.348 AC: 53009AN: 152108Hom.: 9698 Cov.: 32 AF XY: 0.346 AC XY: 25737AN XY: 74350
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969
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3478
ClinVar
Significance: Benign
Submissions summary: Pathogenic:1Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hepatocellular carcinoma Pathogenic:1
Likely risk allele, no assertion criteria provided | case-control | Bioengineering and Technology, Gauhati University | Jul 14, 2022 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 29, 2019 | - - |
Periodontitis Benign:1
Benign, no assertion criteria provided | case-control | Genetics Laboratory, Lanzhou University | Apr 20, 2023 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at