rs2762933

chr20-54153364-T-A

Variant summary

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

The XM_017027692.3(CYP24A1):c.*10+3805A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,200 control chromosomes in the GnomAD database, including 5,775 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 0.26 (5775 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: CYP24A1 XM_017027692.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669

Genes affected

CYP24A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP24A1	XM_017027692.3	c.*10+3805A>T		intron_variant
CYP24A1	XM_047439938.1	c.*10+3805A>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39953 AN: 152082 Hom.: 5769 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.263 AC: 39997 AN: 152200 Hom.: 5775 Cov.: 33 AF XY: 0.267 AC XY: 19865 AN XY: 74422

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.268

Alfa AF: 0.296 Hom.: 843

Bravo AF: 0.242

Asia WGS AF: 0.237 AC: 823 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.45
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2762933; hg19: chr20-52769903;