20-54152812-G-T

Position:

• chr20-54152812-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.*10+4357C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0403 in 152,216 control chromosomes in the GnomAD database, including 191 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 0.040 (191 hom., cov: 32)
• Consequence: CYP24A1 XM_017027692.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

Genes affected

CYP24A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP24A1	XM_017027692.3	c.*10+4357C>A		intron_variant			XP_016883181.1
CYP24A1	XM_047439938.1	c.*10+4357C>A		intron_variant			XP_047295894.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0403 AC: 6132 AN: 152096 Hom.: 192 Cov.: 32

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0877

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0470

Gnomad OTH AF: 0.0458

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

GnomAD4 genome AF: 0.0403 AC: 6132 AN: 152216 Hom.: 191 Cov.: 32 AF XY: 0.0405 AC XY: 3015 AN XY: 74414

Gnomad4 AFR AF: 0.0143

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0877

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0832

Gnomad4 FIN AF: 0.0304

Gnomad4 NFE AF: 0.0470

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0438 Hom.: 161

Bravo AF: 0.0377

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6068810; hg19: chr20-52769351;