chr3:37096024:T>C Detail (hg19) (LRRFIP2)

Information

Genome

Assembly Position
hg19 chr3:37,096,024-37,096,024
hg38 chr3:37,054,533-37,054,533 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_006309.3:c.1951-18A>G
NM_017724.2:c.988-18A>G
NM_001282691.1:c.1297-18A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.554
ToMMo:0.542
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.611

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 614043 OMIM
HGNC 6703 HGNC
Ensembl ENSG00000093167 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv12071159 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
0.082 colorectal carcinoma We previously demonstrated that SNPs (rs1800734, rs749072, and rs13098279) in th... BeFree 23240038 Detail
0.160 colorectal cancer We previously demonstrated that SNPs (rs1800734, rs749072, and rs13098279) in th... BeFree 23240038 Detail
Annotation

Annotations

DescrptionSourceLinks
We previously demonstrated that SNPs (rs1800734, rs749072, and rs13098279) in the MLH1 gene region a... DisGeNET Detail
We previously demonstrated that SNPs (rs1800734, rs749072, and rs13098279) in the MLH1 gene region a... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
Genome
hg19
Position
chr3:37,096,024-37,096,024
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
122.42
Standard deviation of sample read depth (HGVD)
58.12
Number of reference allele (HGVD)
747
Number of alternative allele (HGVD)
927
Allele Frequency (HGVD)
0.553763440860215
Gene Symbol (HGVD)
LRRFIP2
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))
rs749072
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5424
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9091
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8612
East Asian Allele Counts (ExAC)
5266
East Asian Heterozygous Counts (ExAC)
2068
East Asian Homozygous Counts (ExAC)
1599
East Asian Allele Frequency (ExAC)
0.6114723641430562
Chromosome Counts in All Race (ExAC)
121222
Allele Counts in All Race (ExAC)
38811
Heterozygous Counts in All Race (ExAC)
24997
Homozygous Counts in All Race (ExAC)
6907
Allele Frequency in All Race (ExAC)
0.3201646565804887
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