20-54173204-C-G
Position:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000782.5(CYP24A1):c.259-105G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 1,522,238 control chromosomes in the GnomAD database, including 137,756 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.49 ( 19381 hom., cov: 34)
Exomes 𝑓: 0.41 ( 118375 hom. )
Consequence
CYP24A1
NM_000782.5 intron
NM_000782.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.163
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 20-54173204-C-G is Benign according to our data. Variant chr20-54173204-C-G is described in ClinVar as [Benign]. Clinvar id is 1241606.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYP24A1 | NM_000782.5 | c.259-105G>C | intron_variant | ENST00000216862.8 | NP_000773.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP24A1 | ENST00000216862.8 | c.259-105G>C | intron_variant | 1 | NM_000782.5 | ENSP00000216862.3 | ||||
CYP24A1 | ENST00000395955.7 | c.259-105G>C | intron_variant | 1 | ENSP00000379285.3 | |||||
CYP24A1 | ENST00000472970.1 | n.96-105G>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.485 AC: 73771AN: 152102Hom.: 19323 Cov.: 34
GnomAD3 genomes
AF:
AC:
73771
AN:
152102
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.410 AC: 561659AN: 1370018Hom.: 118375 Cov.: 23 AF XY: 0.410 AC XY: 280736AN XY: 684148
GnomAD4 exome
AF:
AC:
561659
AN:
1370018
Hom.:
Cov.:
23
AF XY:
AC XY:
280736
AN XY:
684148
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.485 AC: 73885AN: 152220Hom.: 19381 Cov.: 34 AF XY: 0.481 AC XY: 35777AN XY: 74414
GnomAD4 genome
AF:
AC:
73885
AN:
152220
Hom.:
Cov.:
34
AF XY:
AC XY:
35777
AN XY:
74414
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1467
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at