rs731236
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000376.3(VDR):c.1056T>C(p.Ile352Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,613,190 control chromosomes in the GnomAD database, including 115,868 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000376.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.337 AC: 51104AN: 151662Hom.: 9108 Cov.: 31
GnomAD3 exomes AF: 0.327 AC: 82106AN: 250982Hom.: 14891 AF XY: 0.337 AC XY: 45658AN XY: 135678
GnomAD4 exome AF: 0.376 AC: 549510AN: 1461414Hom.: 106762 Cov.: 71 AF XY: 0.376 AC XY: 273622AN XY: 727036
GnomAD4 genome AF: 0.337 AC: 51113AN: 151776Hom.: 9106 Cov.: 31 AF XY: 0.332 AC XY: 24617AN XY: 74150
ClinVar
Submissions by phenotype
not specified Benign:3
- -
p.Ile352Ile in exon 11 of VDR: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 39.88% (26601/66704) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.b roadinstitute.org; dbSNP rs731236). -
- -
not provided Benign:3
- -
- -
- -
Vitamin D-dependent rickets type II with alopecia Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
- -
Hepatocellular carcinoma Pathogenic:1
- -
Periodontitis Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at