20-54145879-G-T

Position:

• chr20-54145879-G-T

Variant summary

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

The XM_017027692.3(CYP24A1):​c.*599C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,054 control chromosomes in the GnomAD database, including 26,537 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 0.57 (26537 hom., cov: 33)
• Consequence: CYP24A1 XM_017027692.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

Genes affected

CYP24A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP24A1	XM_017027692.3	c.*599C>A		3_prime_UTR_variant	12/12
CYP24A1	XM_047439938.1	c.*599C>A		3_prime_UTR_variant	11/11

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86372 AN: 151936 Hom.: 26499 Cov.: 33

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.569 AC: 86462 AN: 152054 Hom.: 26537 Cov.: 33 AF XY: 0.573 AC XY: 42595 AN XY: 74300

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.552

Alfa AF: 0.470 Hom.: 34290

Bravo AF: 0.573

Asia WGS AF: 0.784 AC: 2725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2762926; hg19: chr20-52762418;