rs2585413

chr20-54145941-G-A

Variant summary

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

The XM_017027692.3(CYP24A1):c.*537C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,124 control chromosomes in the GnomAD database, including 8,746 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 0.34 (8746 hom., cov: 33)
• Consequence: CYP24A1 XM_017027692.3 3_prime_UTR
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP24A1	XM_017027692.3	c.*537C>T		3_prime_UTR_variant	12/12
CYP24A1	XM_047439938.1	c.*537C>T		3_prime_UTR_variant	11/11

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51147 AN: 152006 Hom.: 8743 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.336 AC: 51178 AN: 152124 Hom.: 8746 Cov.: 33 AF XY: 0.343 AC XY: 25519 AN XY: 74376

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.321

Alfa AF: 0.309 Hom.: 3414

Bravo AF: 0.335

Asia WGS AF: 0.412 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.3
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2585413; hg19: chr20-52762480;