Variant rs10623012 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000782.5(CYP24A1):c.*1256_*1257insAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.50 ( 20446 hom., cov: 0)

Exomes 𝑓: 0.36 ( 4 hom. )

Consequence

CYP24A1
NM_000782.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0410

Variant links:

Genes affected

CYP24A1 (HGNC:2602): (cytochrome P450 family 24 subfamily A member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This mitochondrial protein initiates the degradation of 1,25-dihydroxyvitamin D3, the physiologically active form of vitamin D3, by hydroxylation of the side chain. In regulating the level of vitamin D3, this enzyme plays a role in calcium homeostasis and the vitamin D endocrine system. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

CYP24A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 20-54153515-C-CAT is Benign according to our data. Variant chr20-54153515-C-CAT is described in ClinVar as [Benign]. Clinvar id is 338789.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP24A1	NM_000782.5 linkuse as main transcript	c.1256_1257insAT		3_prime_UTR_variant	12/12	ENST00000216862.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP24A1	ENST00000216862.8 linkuse as main transcript	c.1256_1257insAT		3_prime_UTR_variant	12/12	1	NM_000782.5	P1	Q07973-1

Frequencies

GnomAD3 genomes

AF:

0.502

AC:

76107

AN:

151740

Hom.:

20421

Cov.:

show subpopulations

Gnomad AFR

AF:

0.685

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.430

Gnomad ASJ

AF:

0.475

Gnomad EAS

AF:

0.694

Gnomad SAS

AF:

0.656

Gnomad FIN

AF:

0.435

Gnomad MID

AF:

0.455

Gnomad NFE

AF:

0.395

Gnomad OTH

AF:

0.478

GnomAD4 exome

AF:

0.364

AC:

AN:

Hom.:

Cov.:

AF XY:

0.389

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.357

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.502

AC:

76176

AN:

151856

Hom.:

20446

Cov.:

AF XY:

0.507

AC XY:

37636

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.685

Gnomad4 AMR

AF:

0.430

Gnomad4 ASJ

AF:

0.475

Gnomad4 EAS

AF:

0.694

Gnomad4 SAS

AF:

0.654

Gnomad4 FIN

AF:

0.435

Gnomad4 NFE

AF:

0.395

Gnomad4 OTH

AF:

0.483

Alfa

AF:

0.444

Hom.:

1921

Bravo

AF:

0.505

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Infantile hypercalcemia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over