20-54170763-A-G

Position:

• chr20-54170763-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000216862.8(CYP24A1):​c.543+814T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0549 in 152,100 control chromosomes in the GnomAD database, including 314 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 0.055 (314 hom., cov: 32)
• Consequence: CYP24A1 ENST00000216862.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP24A1	NM_000782.5	c.543+814T>C		intron_variant		ENST00000216862.8	NP_000773.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP24A1	ENST00000216862.8	c.543+814T>C		intron_variant		1	NM_000782.5	ENSP00000216862	P1
CYP24A1	ENST00000395954.3	c.117+814T>C		intron_variant		1		ENSP00000379284
CYP24A1	ENST00000395955.7	c.543+814T>C		intron_variant		1		ENSP00000379285

Frequencies

GnomAD3 genomes AF: 0.0550 AC: 8357 AN: 151982 Hom.: 315 Cov.: 32

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0637

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0696

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0780

Gnomad OTH AF: 0.0690

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0549 AC: 8356 AN: 152100 Hom.: 314 Cov.: 32 AF XY: 0.0542 AC XY: 4028 AN XY: 74334

Gnomad4 AFR AF: 0.0148

Gnomad4 AMR AF: 0.0636

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.00310

Gnomad4 SAS AF: 0.0576

Gnomad4 FIN AF: 0.0696

Gnomad4 NFE AF: 0.0780

Gnomad4 OTH AF: 0.0682

Alfa AF: 0.0632 Hom.: 54

Bravo AF: 0.0514

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.91
DANN	Benign	0.43

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: rs13038432; hg19: chr20-52787302;