20-54151852-T-C

Variant summary

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

The XM_017027692.3(CYP24A1):c.*10+5317A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,034 control chromosomes in the GnomAD database, including 2,349 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 0.17 (2349 hom., cov: 32)
• Consequence: CYP24A1 XM_017027692.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

Genes affected

CYP24A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP24A1	XM_017027692.3	c.*10+5317A>G		intron_variant
CYP24A1	XM_047439938.1	c.*10+5317A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25875 AN: 151916 Hom.: 2345 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.170 AC: 25920 AN: 152034 Hom.: 2349 Cov.: 32 AF XY: 0.176 AC XY: 13049 AN XY: 74324

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.177

Alfa AF: 0.157 Hom.: 2656

Bravo AF: 0.161

Asia WGS AF: 0.224 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.5
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2762932; hg19: chr20-52768391;