rs2762929

Positions:

• chr20-54149656-T-C
• chr20-54149656-T-G

Variant summary

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

The XM_017027692.3(CYP24A1):​c.*11-3189A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,826 control chromosomes in the GnomAD database, including 20,499 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 0.50 (20499 hom., cov: 31)
• Consequence: CYP24A1 XM_017027692.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

Genes affected

CYP24A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP24A1	XM_017027692.3	c.*11-3189A>G		intron_variant			XP_016883181.1
CYP24A1	XM_047439938.1	c.*11-3189A>G		intron_variant			XP_047295894.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76037 AN: 151704 Hom.: 20474 Cov.: 31

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.501 AC: 76107 AN: 151826 Hom.: 20499 Cov.: 31 AF XY: 0.506 AC XY: 37525 AN XY: 74144

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.482

Alfa AF: 0.429 Hom.: 11313

Bravo AF: 0.505

Asia WGS AF: 0.668 AC: 2322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2762929; hg19: chr20-52766195;