NM_000782.5:c.991-1107C>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000782.5(CYP24A1):c.991-1107C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,156 control chromosomes in the GnomAD database, including 7,267 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 0.29 ( 7267 hom., cov: 33)
Consequence
CYP24A1
NM_000782.5 intron
NM_000782.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.450
Publications
2 publications found
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 Gene-Disease associations (from GenCC):
- hypercalcemia, infantile, 1Inheritance: AR Classification: STRONG, LIMITED Submitted by: G2P, Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)
- autosomal recessive infantile hypercalcemiaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.290 AC: 44032AN: 152038Hom.: 7260 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
44032
AN:
152038
Hom.:
Cov.:
33
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.290 AC: 44060AN: 152156Hom.: 7267 Cov.: 33 AF XY: 0.292 AC XY: 21741AN XY: 74380 show subpopulations
GnomAD4 genome
AF:
AC:
44060
AN:
152156
Hom.:
Cov.:
33
AF XY:
AC XY:
21741
AN XY:
74380
show subpopulations
African (AFR)
AF:
AC:
17102
AN:
41500
American (AMR)
AF:
AC:
4180
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
796
AN:
3472
East Asian (EAS)
AF:
AC:
3139
AN:
5184
South Asian (SAS)
AF:
AC:
1706
AN:
4826
European-Finnish (FIN)
AF:
AC:
2155
AN:
10576
Middle Eastern (MID)
AF:
AC:
59
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14225
AN:
67988
Other (OTH)
AF:
AC:
562
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1581
3162
4742
6323
7904
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
448
896
1344
1792
2240
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1502
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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