chr5:79950781:A>G Detail (hg19) (DHFR, MSH3)

Information

Genome

Assembly Position
hg19 chr5:79,950,781-79,950,781
hg38 chr5:80,654,962-80,654,962 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000791.3:c.-473T>C
Ensemble ENST00000439211.7:c.-473T>C
Type Transcript Protein
RefSeq NM_002439.4:c.235A>G NP_002430.3:p.Ile79Val
Ensemble ENST00000265081.7:c.235A>G ENST00000265081.7:p.Ile79Val
ENST00000667069.1:c.235A>G ENST00000667069.1:p.Ile79Val
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.736
ToMMo:0.711
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.875

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 126060 OMIM
HGNC 2861 HGNC
Ensembl ENSG00000228716 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv21673126 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 600887 OMIM
HGNC 7326 HGNC
Ensembl ENSG00000113318 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv21673126 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-03-28 criteria provided, single submitter not specified germline Detail
Benign 2021-02-19 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2023-11-29 criteria provided, single submitter Constitutional megaloblastic anemia with severe neurologic disease germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.004 Non-small cell lung carcinoma Variant alleles were significantly associated with favorable survivals of NSCLC ... BeFree 20737570 Detail
0.003 Non-small cell lung carcinoma Variant alleles were significantly associated with favorable survivals of NSCLC ... BeFree 20737570 Detail
0.003 Non-small cell lung carcinoma Variant alleles were significantly associated with favorable survivals of NSCLC ... BeFree 20737570 Detail
0.003 Non-small cell lung carcinoma Variant alleles were significantly associated with favorable survivals of NSCLC ... BeFree 20737570 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000791.4(DHFR):c.-473T>C AND not specified ClinVar Detail
NM_000791.4(DHFR):c.-473T>C AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000791.4(DHFR):c.-473T>C AND Constitutional megaloblastic anemia with severe neurologic disease ClinVar Detail
NM_000791.4(DHFR):c.-473T>C AND not provided ClinVar Detail
Variant alleles were significantly associated with favorable survivals of NSCLC for MTR rs3768160 A&... DisGeNET Detail
Variant alleles were significantly associated with favorable survivals of NSCLC for MTR rs3768160 A&... DisGeNET Detail
Variant alleles were significantly associated with favorable survivals of NSCLC for MTR rs3768160 A&... DisGeNET Detail
Variant alleles were significantly associated with favorable survivals of NSCLC for MTR rs3768160 A&... 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
rs1650697 dbSNP
Genome
hg19
Position
chr5:79,950,781-79,950,781
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1097
Mean of sample read depth (HGVD)
26.96
Standard deviation of sample read depth (HGVD)
12.92
Number of reference allele (HGVD)
580
Number of alternative allele (HGVD)
1614
Allele Frequency (HGVD)
0.7356426618049225
Gene Symbol (HGVD)
MSH3
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))
rs1650697
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.7114
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11911
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16744
East Asian Chromosome Counts (ExAC)
120
East Asian Allele Counts (ExAC)
105
East Asian Heterozygous Counts (ExAC)
15
East Asian Homozygous Counts (ExAC)
45
East Asian Allele Frequency (ExAC)
0.875
Chromosome Counts in All Race (ExAC)
12098
Allele Counts in All Race (ExAC)
10923
Heterozygous Counts in All Race (ExAC)
967
Homozygous Counts in All Race (ExAC)
4978
Allele Frequency in All Race (ExAC)
0.902876508513804
Genome browser