rs17878969

Positions:

• chr12-47842623-ATTTTTTTTTT-A
• chr12-47842623-ATTTTTTTTTT-AT
• chr12-47842623-ATTTTTTTTTT-ATT
• chr12-47842623-ATTTTTTTTTT-ATTT
• chr12-47842623-ATTTTTTTTTT-ATTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
• chr12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000376.3(VDR):​c.*2113_*2122del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Failed GnomAD Quality Control
• Consequence: VDR NM_000376.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.759

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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VDR	NM_000376.3	c.*2113_*2122del		3_prime_UTR_variant	10/10	ENST00000549336.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VDR	ENST00000549336.6	c.*2113_*2122del		3_prime_UTR_variant	10/10	1	NM_000376.3	P1
VDR	ENST00000550325.5			3_prime_UTR_variant	10/10	1
VDR	ENST00000229022.9			3_prime_UTR_variant	8/8	5
VDR	ENST00000395324.6	c.*2113_*2122del		3_prime_UTR_variant	10/10	5		P1

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17878969; hg19: chr12-48236406;