rs6091828
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000782.5(CYP24A1):c.990+46C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0425 in 1,222,902 control chromosomes in the GnomAD database, including 1,960 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.071 ( 612 hom., cov: 30)
Exomes 𝑓: 0.039 ( 1348 hom. )
Consequence
CYP24A1
NM_000782.5 intron
NM_000782.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0480
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 20-54162671-G-T is Benign according to our data. Variant chr20-54162671-G-T is described in ClinVar as [Benign]. Clinvar id is 1174391.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYP24A1 | NM_000782.5 | c.990+46C>A | intron_variant | ENST00000216862.8 | NP_000773.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP24A1 | ENST00000216862.8 | c.990+46C>A | intron_variant | 1 | NM_000782.5 | ENSP00000216862.3 | ||||
CYP24A1 | ENST00000395955.7 | c.990+46C>A | intron_variant | 1 | ENSP00000379285.3 | |||||
CYP24A1 | ENST00000395954.3 | c.564+46C>A | intron_variant | 1 | ENSP00000379284.3 | |||||
CYP24A1 | ENST00000487593.1 | n.289C>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0709 AC: 10485AN: 147782Hom.: 609 Cov.: 30
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GnomAD3 exomes AF: 0.0559 AC: 14037AN: 251292Hom.: 609 AF XY: 0.0553 AC XY: 7510AN XY: 135830
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GnomAD4 exome AF: 0.0386 AC: 41484AN: 1075004Hom.: 1348 Cov.: 15 AF XY: 0.0402 AC XY: 22213AN XY: 552892
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GnomAD4 genome AF: 0.0711 AC: 10513AN: 147898Hom.: 612 Cov.: 30 AF XY: 0.0735 AC XY: 5304AN XY: 72152
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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 10, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at