rs8118441

Positions:

• chr20-54149846-T-A

Variant summary

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

The XM_017027692.3(CYP24A1):​c.*11-3379A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,136 control chromosomes in the GnomAD database, including 3,214 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 0.19 (3214 hom., cov: 32)
• Consequence: CYP24A1 XM_017027692.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

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 = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP24A1	XM_017027692.3	c.*11-3379A>T		intron_variant
CYP24A1	XM_047439938.1	c.*11-3379A>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29019 AN: 152020 Hom.: 3212 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.191 AC: 29028 AN: 152136 Hom.: 3214 Cov.: 32 AF XY: 0.191 AC XY: 14217 AN XY: 74380

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.168

Alfa AF: 0.171 Hom.: 285

Bravo AF: 0.202

Asia WGS AF: 0.201 AC: 700 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	2.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8118441; hg19: chr20-52766385;