20-54149546-A-T

Position:

• chr20-54149546-A-T

Variant summary

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

The XM_017027692.3(CYP24A1):​c.*11-3079T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,218 control chromosomes in the GnomAD database, including 1,580 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 0.14 (1580 hom., cov: 32)
• Consequence: CYP24A1 XM_017027692.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP24A1	XM_017027692.3	c.*11-3079T>A		intron_variant			XP_016883181.1
CYP24A1	XM_047439938.1	c.*11-3079T>A		intron_variant			XP_047295894.1
		n.54149546A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20759 AN: 152100 Hom.: 1582 Cov.: 32

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.136 AC: 20767 AN: 152218 Hom.: 1580 Cov.: 32 AF XY: 0.143 AC XY: 10613 AN XY: 74422

Gnomad4 AFR AF: 0.0839

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.0998

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.148

Alfa AF: 0.0616 Hom.: 67

Bravo AF: 0.123

Asia WGS AF: 0.210 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.79
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2762928; hg19: chr20-52766085;