12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTT

Variant summary

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

The NM_000376.3(VDR):​c.*2122_*2123insAAAAAAAA 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: 𝑓 0.00034 ( 0 hom., cov: 0)

Consequence

VDR
NM_000376.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.933
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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
VDRNM_000376.3 linkuse as main transcriptc.*2122_*2123insAAAAAAAA 3_prime_UTR_variant 10/10 ENST00000549336.6 NP_000367.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
VDRENST00000549336.6 linkuse as main transcriptc.*2122_*2123insAAAAAAAA 3_prime_UTR_variant 10/101 NM_000376.3 ENSP00000449573 P1P11473-1
VDRENST00000395324.6 linkuse as main transcriptc.*2122_*2123insAAAAAAAA 3_prime_UTR_variant 10/105 ENSP00000378734 P1P11473-1
VDRENST00000550325.5 linkuse as main transcript downstream_gene_variant 1 ENSP00000447173 P11473-2
VDRENST00000229022.9 linkuse as main transcript downstream_gene_variant 5 ENSP00000229022

Frequencies

GnomAD3 genomes
AF:
0.000343
AC:
45
AN:
131050
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000237
Gnomad AMI
AF:
0.00117
Gnomad AMR
AF:
0.000155
Gnomad ASJ
AF:
0.000608
Gnomad EAS
AF:
0.000468
Gnomad SAS
AF:
0.000245
Gnomad FIN
AF:
0.000327
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000424
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
0
GnomAD4 genome
AF:
0.000343
AC:
45
AN:
131050
Hom.:
0
Cov.:
0
AF XY:
0.000290
AC XY:
18
AN XY:
62012
show subpopulations
Gnomad4 AFR
AF:
0.000237
Gnomad4 AMR
AF:
0.000155
Gnomad4 ASJ
AF:
0.000608
Gnomad4 EAS
AF:
0.000468
Gnomad4 SAS
AF:
0.000245
Gnomad4 FIN
AF:
0.000327
Gnomad4 NFE
AF:
0.000424
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs17878969; hg19: chr12-48236406; API