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rs4516035

Variant summary

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

The ENST00000622535.1(null):n.922T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,162 control chromosomes in the GnomAD database, including 9,081 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 0.31 ( 9079 hom., cov: 33)
Exomes 𝑓: 0.50 ( 2 hom. )

Consequence


ENST00000622535.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0800
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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 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
ENST00000622535.1 linkuse as main transcriptn.922T>C non_coding_transcript_exon_variant 1/1
VDRENST00000395324.6 linkuse as main transcriptc.-83-23269A>G intron_variant 5 P1P11473-1

Frequencies

GnomAD3 genomes
AF:
0.305
AC:
46411
AN:
152036
Hom.:
9077
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0856
Gnomad AMI
AF:
0.425
Gnomad AMR
AF:
0.308
Gnomad ASJ
AF:
0.341
Gnomad EAS
AF:
0.0217
Gnomad SAS
AF:
0.231
Gnomad FIN
AF:
0.475
Gnomad MID
AF:
0.375
Gnomad NFE
AF:
0.435
Gnomad OTH
AF:
0.315
GnomAD4 exome
AF:
0.500
AC:
4
AN:
8
Hom.:
2
Cov.:
0
AF XY:
0.500
AC XY:
4
AN XY:
8
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.305
AC:
46427
AN:
152154
Hom.:
9079
Cov.:
33
AF XY:
0.305
AC XY:
22689
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.0855
Gnomad4 AMR
AF:
0.308
Gnomad4 ASJ
AF:
0.341
Gnomad4 EAS
AF:
0.0224
Gnomad4 SAS
AF:
0.233
Gnomad4 FIN
AF:
0.475
Gnomad4 NFE
AF:
0.435
Gnomad4 OTH
AF:
0.315
Alfa
AF:
0.398
Hom.:
26527
Bravo
AF:
0.282
Asia WGS
AF:
0.159
AC:
553
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
Cadd
Benign
4.2
Dann
Benign
0.65

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: rs4516035; hg19: chr12-48299826; API