chr2:38075247:G>C Detail (hg38) (CYP1B1)

Information

Genome

Assembly Position
hg19 chr2:38,302,390-38,302,390 View the variant detail on this assembly version.
hg38 chr2:38,075,247-38,075,247

HGVS

Type Transcript Protein
RefSeq NM_000104.3:c.142C>G NP_000095.2:p.Arg48Gly
Ensemble ENST00000490576.2:c.142C>G ENST00000490576.2:p.Arg48Gly
ENST00000494864.1:c.-70-3937C>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.114
ToMMo:0.112
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.233

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601771 OMIM
HGNC 2597 HGNC
Ensembl ENSG00000138061 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6524298 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2021-12-03 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-07-30 criteria provided, multiple submitters, no conflicts Glaucoma 3A germline Detail
Benign 2024-02-01 criteria provided, single submitter Congenital glaucoma germline Detail
Benign 2021-07-30 criteria provided, single submitter anterior segment dysgenesis 6 germline Detail
Benign 2015-03-03 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Non-small cell lung carcinoma When we corrected for multiple testing using these statistical tools, three nove... BeFree 18258609 Detail
0.104 Malignant neoplasm of breast To examine the association between six SNPs, CYP1A1(*)2A, CYP1A1(*)2C, CYP1A2(*)... BeFree 19229255 Detail
0.024 breast carcinoma To examine the association between six SNPs, CYP1A1(*)2A, CYP1A1(*)2C, CYP1A2(*)... BeFree 19229255 Detail
<0.001 Non-small cell lung carcinoma When we corrected for multiple testing using these statistical tools, three nove... BeFree 18258609 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000104.4(CYP1B1):c.142C>G (p.Arg48Gly) AND not specified ClinVar Detail
NM_000104.4(CYP1B1):c.142C>G (p.Arg48Gly) AND Glaucoma 3A ClinVar Detail
NM_000104.4(CYP1B1):c.142C>G (p.Arg48Gly) AND Congenital glaucoma ClinVar Detail
NM_000104.4(CYP1B1):c.142C>G (p.Arg48Gly) AND Anterior segment dysgenesis 6 ClinVar Detail
NM_000104.4(CYP1B1):c.142C>G (p.Arg48Gly) AND not provided ClinVar Detail
When we corrected for multiple testing using these statistical tools, three novel associations of NS... DisGeNET Detail
To examine the association between six SNPs, CYP1A1(*)2A, CYP1A1(*)2C, CYP1A2(*)1F, CYP1B1 Arg(48)Gl... DisGeNET Detail
To examine the association between six SNPs, CYP1A1(*)2A, CYP1A1(*)2C, CYP1A2(*)1F, CYP1B1 Arg(48)Gl... DisGeNET Detail
When we corrected for multiple testing using these statistical tools, three novel associations of NS... 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
rs10012 dbSNP
Genome
hg38
Position
chr2:38,075,247-38,075,247
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1160
Mean of sample read depth (HGVD)
44.98
Standard deviation of sample read depth (HGVD)
21.46
Number of reference allele (HGVD)
2056
Number of alternative allele (HGVD)
264
Allele Frequency (HGVD)
0.11379310344827587
Gene Symbol (HGVD)
CYP1B1
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))
rs10012
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1116
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1870
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
5074
East Asian Allele Counts (ExAC)
1180
East Asian Heterozygous Counts (ExAC)
990
East Asian Homozygous Counts (ExAC)
95
East Asian Allele Frequency (ExAC)
0.23255813953488372
Chromosome Counts in All Race (ExAC)
77386
Allele Counts in All Race (ExAC)
29232
Heterozygous Counts in All Race (ExAC)
19686
Homozygous Counts in All Race (ExAC)
4773
Allele Frequency in All Race (ExAC)
0.3777427441656114
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