chr6:32006387:A>T Detail (hg19) (CYP21A2, LOC106780800)

Information

Genome

Assembly Position
hg19 chr6:32,006,387-32,006,387
hg38 chr6:32,038,610-32,038,610 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000435122.3:c.188A>T ENST00000435122.3:p.His63Leu
ENST00000644719.2:c.188A>T ENST00000644719.2:p.His63Leu
Summary

MGeND

Clinical significance Pathogenic
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.095
ToMMo:0.058
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.318

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 613815 OMIM
HGNC 2600 HGNC
Ensembl ENSG00000231852 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24809583 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other germline MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-05-28 criteria provided, single submitter Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency germline unknown Detail
Benign 2015-02-23 criteria provided, single submitter not specified germline Detail
Likely pathogenic 2022-10-01 criteria provided, single submitter congenital adrenal hyperplasia germline Detail
Pathogenic 2022-09-28 criteria provided, multiple submitters, no conflicts not provided unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.155 21-hydroxylase deficiency p.H62L, a rare mutation of the CYP21 gene identified in two forms of 21-hydroxyl... BeFree 18319307 Detail
0.303 Congenital adrenal hyperplasia due to 21 hydroxylase deficiency p.H62L, a rare mutation of the CYP21 gene identified in two forms of 21-hydroxyl... BeFree 18319307 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000500.9(CYP21A2):c.188A>T (p.His63Leu) AND Classic congenital adrenal hyperplasia due to 21-hydr... ClinVar Detail
NM_000500.9(CYP21A2):c.188A>T (p.His63Leu) AND not specified ClinVar Detail
NM_000500.9(CYP21A2):c.188A>T (p.His63Leu) AND Congenital adrenal hyperplasia ClinVar Detail
NM_000500.9(CYP21A2):c.188A>T (p.His63Leu) AND not provided ClinVar Detail
p.H62L, a rare mutation of the CYP21 gene identified in two forms of 21-hydroxylase deficiency. DisGeNET Detail
p.H62L, a rare mutation of the CYP21 gene identified in two forms of 21-hydroxylase deficiency. 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
rs9378252 dbSNP
Genome
hg19
Position
chr6:32,006,387-32,006,387
Variant Type
snv
Reference Allele
A
Alternative Allele
T
Filtering Status (HGVD)
LowQual
Filtering Status (HGVD)
VQSRTrancheSNP99.00to99.90
# of samples (HGVD)
467
Mean of sample read depth (HGVD)
5.20
Standard deviation of sample read depth (HGVD)
11.12
Number of reference allele (HGVD)
845
Number of alternative allele (HGVD)
89
Allele Frequency (HGVD)
0.09528907922912205
Gene Symbol (HGVD)
CYP21A2
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
VQSRTrancheSNP99.80to99.90
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs9378252
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0582
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
976
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
1848
East Asian Allele Counts (ExAC)
587
East Asian Heterozygous Counts (ExAC)
587
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.31764069264069267
Chromosome Counts in All Race (ExAC)
24818
Allele Counts in All Race (ExAC)
2325
Heterozygous Counts in All Race (ExAC)
2325
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
0.0936820049963736
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