chr20:52786219:G>A Detail (hg19) (CYP24A1)

Information

Genome

Assembly Position
hg19 chr20:52,786,219-52,786,219
hg38 chr20:54,169,680-54,169,680 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000782.4:c.552C>T NP_000773.2:p.Ala184=
NM_001128915.1:c.552C>T NP_001122387.1:p.Ala184=
Ensemble ENST00000216862.8:c.552C>T ENST00000216862.8:p.Ala184=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.474
ToMMo:0.459
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.421

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 126065 OMIM
HGNC 2602 HGNC
Ensembl ENSG00000019186 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv64082973 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-07-30 criteria provided, multiple submitters, no conflicts Hypercalcemia, infantile, 1 germline Detail
Benign 2016-03-21 criteria provided, single submitter not specified germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Papillary thyroid carcinoma German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... BeFree 22690899 Detail
<0.001 Papillary thyroid carcinoma German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... BeFree 22690899 Detail
<0.001 differentiated thyroid gland carcinoma German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... BeFree 22690899 Detail
0.001 differentiated thyroid gland carcinoma German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... BeFree 22690899 Detail
<0.001 Follicular thyroid carcinoma German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... BeFree 22690899 Detail
0.020 Papillary thyroid carcinoma German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... BeFree 22690899 Detail
<0.001 Papillary thyroid carcinoma German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... BeFree 22690899 Detail
0.004 Follicular thyroid carcinoma German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... BeFree 22690899 Detail
<0.001 Follicular thyroid carcinoma German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... BeFree 22690899 Detail
<0.001 Follicular thyroid carcinoma German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... BeFree 22690899 Detail
<0.001 differentiated thyroid gland carcinoma German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicul... BeFree 22690899 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000782.5(CYP24A1):c.552C>T (p.Ala184=) AND Hypercalcemia, infantile, 1 ClinVar Detail
NM_000782.5(CYP24A1):c.552C>T (p.Ala184=) AND not specified ClinVar Detail
NM_000782.5(CYP24A1):c.552C>T (p.Ala184=) AND not provided ClinVar Detail
German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... DisGeNET Detail
German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... DisGeNET Detail
German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... DisGeNET Detail
German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... DisGeNET Detail
German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... DisGeNET Detail
German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... DisGeNET Detail
German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... DisGeNET Detail
German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... DisGeNET Detail
German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... DisGeNET Detail
German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... DisGeNET Detail
German patients (n=253) with DTC (papillary thyroid carcinoma [PTC] and follicular thyroid carcinoma... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2296241 dbSNP
Genome
hg19
Position
chr20:52,786,219-52,786,219
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
131.39
Standard deviation of sample read depth (HGVD)
58.98
Number of reference allele (HGVD)
1273
Number of alternative allele (HGVD)
1147
Allele Frequency (HGVD)
0.47396694214876034
Gene Symbol (HGVD)
CYP24A1
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs2296241
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4593
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7698
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8626
East Asian Allele Counts (ExAC)
3633
East Asian Heterozygous Counts (ExAC)
2093
East Asian Homozygous Counts (ExAC)
770
East Asian Allele Frequency (ExAC)
0.42116856016693716
Chromosome Counts in All Race (ExAC)
121252
Allele Counts in All Race (ExAC)
59699
Heterozygous Counts in All Race (ExAC)
29687
Homozygous Counts in All Race (ExAC)
15006
Allele Frequency in All Race (ExAC)
0.49235476528222216
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