chr5:79126136:G>A Detail (hg38) (BHMT)

Information

Genome

Assembly Position
hg19 chr5:78,421,959-78,421,959 View the variant detail on this assembly version.
hg38 chr5:79,126,136-79,126,136

HGVS

Type Transcript Protein
RefSeq NM_001713.2:c.716G>A NP_001704.2:p.Arg239Gln
Ensemble ENST00000274353.10:c.716G>A ENST00000274353.10:p.Arg239Gln
ENST00000524080.1:c.257G>A ENST00000524080.1:p.Arg86Gln
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.216
ToMMo:0.214
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.321

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 602888 OMIM
HGNC 1047 HGNC
Ensembl ENSG00000145692 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv21633359 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 cervix carcinoma Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239G... BeFree 21349258 Detail
0.004 ovarian carcinoma Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)... BeFree 22183302 Detail
0.013 Malignant neoplasm of ovary Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)... BeFree 22183302 Detail
0.006 Malignant tumor of cervix Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239G... BeFree 21349258 Detail
<0.001 ovarian carcinoma Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)... BeFree 22183302 Detail
0.001 Malignant tumor of cervix Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239G... BeFree 21349258 Detail
0.003 Malignant neoplasm of ovary Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)... BeFree 22183302 Detail
0.010 cervix carcinoma Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239G... BeFree 21349258 Detail
<0.001 breast carcinoma The betaine-homocysteine methyltransferase gene (BHMT) rs3733890 polymorphism wa... BeFree 19635752 Detail
0.003 Malignant neoplasm of breast The betaine-homocysteine methyltransferase gene (BHMT) rs3733890 polymorphism wa... BeFree 19635752 Detail
<0.001 breast carcinoma The BHMT rs3733890 polymorphism was also examined but was found not to be associ... BeFree 18230680 Detail
0.003 Malignant neoplasm of breast The BHMT rs3733890 polymorphism was also examined but was found not to be associ... BeFree 18230680 Detail
0.125 Neural Tube Defects [BHMT rs3733890 is significantly associated in our data set, whereas MTHFR rs180... GAD 17035141 Detail
<0.001 Adenoma of large intestine We observed significant evidence for departure from multiplicative interaction f... BeFree 17389618 Detail
0.020 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
0.010 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
0.008 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
0.005 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
<0.001 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
Annotation

Annotations

DescrptionSourceLinks
Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239Gln (rs3733890), MTR ... DisGeNET Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)... DisGeNET Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)... DisGeNET Detail
Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239Gln (rs3733890), MTR ... DisGeNET Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)... DisGeNET Detail
Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239Gln (rs3733890), MTR ... DisGeNET Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)... DisGeNET Detail
Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239Gln (rs3733890), MTR ... DisGeNET Detail
The betaine-homocysteine methyltransferase gene (BHMT) rs3733890 polymorphism was associated with re... DisGeNET Detail
The betaine-homocysteine methyltransferase gene (BHMT) rs3733890 polymorphism was associated with re... DisGeNET Detail
The BHMT rs3733890 polymorphism was also examined but was found not to be associated with breast can... DisGeNET Detail
The BHMT rs3733890 polymorphism was also examined but was found not to be associated with breast can... DisGeNET Detail
[BHMT rs3733890 is significantly associated in our data set, whereas MTHFR rs1801133 is not a major ... DisGeNET Detail
We observed significant evidence for departure from multiplicative interaction for the betaine-homoc... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... 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
-
Genome
hg38
Position
chr5:79,126,136-79,126,136
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
127.58
Standard deviation of sample read depth (HGVD)
60.20
Number of reference allele (HGVD)
1895
Number of alternative allele (HGVD)
523
Allele Frequency (HGVD)
0.2162944582299421
Gene Symbol (HGVD)
BHMT
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))
rs3733890
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2138
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3584
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8634
East Asian Allele Counts (ExAC)
2774
East Asian Heterozygous Counts (ExAC)
1866
East Asian Homozygous Counts (ExAC)
454
East Asian Allele Frequency (ExAC)
0.32128793143386614
Chromosome Counts in All Race (ExAC)
121272
Allele Counts in All Race (ExAC)
35808
Heterozygous Counts in All Race (ExAC)
24776
Homozygous Counts in All Race (ExAC)
5516
Allele Frequency in All Race (ExAC)
0.295270136552543
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