rs6097805

Positions:

• chr20-54151957-A-G

Variant summary

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

The XM_017027692.3(CYP24A1):​c.*10+5212T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,992 control chromosomes in the GnomAD database, including 9,296 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 0.33 (9296 hom., cov: 32)
• Consequence: CYP24A1 XM_017027692.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

Genes affected

CYP24A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP24A1	XM_017027692.3	c.*10+5212T>C		intron_variant			XP_016883181.1
CYP24A1	XM_047439938.1	c.*10+5212T>C		intron_variant			XP_047295894.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50202 AN: 151874 Hom.: 9290 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.330 AC: 50227 AN: 151992 Hom.: 9296 Cov.: 32 AF XY: 0.331 AC XY: 24578 AN XY: 74292

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.306

Alfa AF: 0.290 Hom.: 1350

Bravo AF: 0.344

Asia WGS AF: 0.430 AC: 1494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6097805; hg19: chr20-52768496;