rs2762934

Variant names:

• chr20-54154722-G-A
• rs2762934
• NM_000782.5:c.*50C>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000782.5(CYP24A1):​c.*50C>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 0.181 in 153,476 control chromosomes in the GnomAD database, including 2,635 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.18 (2594 hom., cov: 29)
  • Exomes 𝑓: 0.21 (41 hom.)
• Consequence: CYP24A1 NM_000782.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.100

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 20-54154722-G-A is Benign according to our data. Variant chr20-54154722-G-A is described in ClinVar as [Benign]. Clinvar id is 338810.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-54154722-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP24A1	NM_000782.5	c.*50C>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.*50C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_000782.5	ENSP00000216862.3
CYP24A1	ENST00000395955	c.*50C>T		3_prime_UTR_variant	Exon 11 of 11	1		ENSP00000379285.3
CYP24A1	ENST00000395954	c.*50C>T		3_prime_UTR_variant	Exon 10 of 10	1		ENSP00000379284.3
CYP24A1	ENST00000460643.1	n.342C>T		non_coding_transcript_exon_variant	Exon 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27460 AN: 151716 Hom.: 2597 Cov.: 29

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.215 AC: 353 AN: 1642 Hom.: 41 Cov.: 0 AF XY: 0.214 AC XY: 185 AN XY: 866

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.114

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.131

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.263

Gnomad4 NFE exome AF: 0.225

Gnomad4 OTH exome AF: 0.139

GnomAD4 genome AF: 0.181 AC: 27471 AN: 151834 Hom.: 2594 Cov.: 29 AF XY: 0.185 AC XY: 13716 AN XY: 74176

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.196

Alfa AF: 0.186 Hom.: 5893

Bravo AF: 0.172

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercalcemia, infantile, 1 Benign:1

Jan 12, 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. -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2762934; hg19: chr20-52771261;