chr17:61995030:A>T Detail (hg19) (GH1, GH-LCR)

Information

Genome

Assembly Position
hg19 chr17:61,995,030-61,995,030
hg38 chr17:63,917,670-63,917,670 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_022560.3:c.336+90T>A
NM_022559.3:c.411+90T>A
NM_000515.4:c.456+90T>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.433
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 139250 OMIM
HGNC 4261 HGNC
Ensembl ENSG00000259384 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv58380409 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-11-12 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Polyp of large intestine We examined the risk of colorectal polyps in relation to body size factors and c... BeFree 20580999 Detail
<0.001 Polyp of large intestine We examined the risk of colorectal polyps in relation to body size factors and c... BeFree 20580999 Detail
0.011 colorectal cancer A common polymorphism in the GH1 gene, rs2665802, was previously shown to be ass... BeFree 19064544 Detail
0.002 colorectal carcinoma A common polymorphism in the GH1 gene, rs2665802, was previously shown to be ass... BeFree 19064544 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000515.5(GH1):c.456+90T>A AND not provided ClinVar Detail
We examined the risk of colorectal polyps in relation to body size factors and candidate polymorphis... DisGeNET Detail
We examined the risk of colorectal polyps in relation to body size factors and candidate polymorphis... DisGeNET Detail
A common polymorphism in the GH1 gene, rs2665802, was previously shown to be associated with lower I... DisGeNET Detail
A common polymorphism in the GH1 gene, rs2665802, was previously shown to be associated with lower I... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2665802 dbSNP
Genome
hg19
Position
chr17:61,995,030-61,995,030
Variant Type
snv
Reference Allele
A
Alternative Allele
T
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))
rs2665802
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.433
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7257
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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