20-54153900-G-A

Variant names:

• chr20-54153900-G-A
• rs11907350
• NM_000782.5:c.*872C>T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000782.5(CYP24A1):​c.*872C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,480 control chromosomes in the GnomAD database, including 705 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.067 (705 hom., cov: 33)
  • Exomes 𝑓: 0.032 (0 hom.)
• Consequence: CYP24A1 NM_000782.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.29

Genes affected

CYP24A1 (HGNC:2602): (cytochrome P450 family 24 subfamily A member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This mitochondrial protein initiates the degradation of 1,25-dihydroxyvitamin D3, the physiologically active form of vitamin D3, by hydroxylation of the side chain. In regulating the level of vitamin D3, this enzyme plays a role in calcium homeostasis and the vitamin D endocrine system. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 20-54153900-G-A is Benign according to our data. Variant chr20-54153900-G-A is described in ClinVar as [Benign]. Clinvar id is 338794.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP24A1	NM_000782.5	c.*872C>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000216862.8	NP_000773.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP24A1	ENST00000216862	c.*872C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_000782.5	ENSP00000216862.3
CYP24A1	ENST00000395955.7	c.*872C>T		downstream_gene_variant		1		ENSP00000379285.3

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10138 AN: 152016 Hom.: 706 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0354

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.0381

Gnomad MID AF: 0.0321

Gnomad NFE AF: 0.0250

Gnomad OTH AF: 0.0642

GnomAD4 exome AF: 0.0318 AC: 11 AN: 346 Hom.: 0 Cov.: 0 AF XY: 0.0340 AC XY: 7 AN XY: 206

Gnomad4 FIN exome AF: 0.0324

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0667 AC: 10145 AN: 152134 Hom.: 705 Cov.: 33 AF XY: 0.0659 AC XY: 4899 AN XY: 74366

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0354

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00415

Gnomad4 FIN AF: 0.0381

Gnomad4 NFE AF: 0.0249

Gnomad4 OTH AF: 0.0636

Alfa AF: 0.0351 Hom.: 178

Bravo AF: 0.0709

Asia WGS AF: 0.0130 AC: 46 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hypercalcemia, infantile, 1 Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.15
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11907350; hg19: chr20-52770439;