chr17:648186:G>A Detail (hg19) (GEMIN4)

Information

Genome

Assembly Position
hg19 chr17:648,186-648,186
hg38 chr17:744,946-744,946 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_015721.2:c.3097C>T NP_056536.2:p.Arg1033Cys
Ensemble ENST00000576778.1:c.3064C>T ENST00000576778.1:p.Arg1022Cys
ENST00000319004.6:c.3097C>T ENST00000319004.6:p.Arg1033Cys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.665
ToMMo:0.660
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.701

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606969 OMIM
HGNC 15717 HGNC
Ensembl ENSG00000179409 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv56684225 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2020-11-03 criteria provided, single submitter not provided germline Detail
Benign 2021-07-14 criteria provided, single submitter neurodevelopmental disorder with microcephaly, cataracts, and renal abnormalities germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 esophageal carcinoma To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
0.003 Malignant neoplasm of esophagus To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
<0.001 Esophageal Neoplasms To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
<0.001 Squamous cell carcinoma of esophagus To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
0.005 Malignant neoplasm of esophagus To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
<0.001 Malignant neoplasm of esophagus To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
<0.001 esophageal carcinoma To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
<0.001 Squamous cell carcinoma of esophagus To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
0.003 Malignant neoplasm of esophagus To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
0.003 Esophageal Neoplasms To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
<0.001 Esophageal Neoplasms To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
<0.001 Esophageal Neoplasms To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
<0.001 esophageal carcinoma To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
<0.001 esophageal carcinoma To evaluate the association between microRNA-related SNPs and EC, a case-control... BeFree 24916311 Detail
<0.001 Hepatitis B, Chronic To explore the relationship between three SNPs (rs3757 in DGCR8, rs636832 in AGO... BeFree 25239527 Detail
<0.001 malignant peripheral nerve sheath tumor Four SNPs (DDX5 rs1991401, OR=1.79, 95% CI, 1.34-2.38, P=7.90 × 10(-5); DROSHA r... BeFree 23763827 Detail
<0.001 malignant peripheral nerve sheath tumor Four SNPs (DDX5 rs1991401, OR=1.79, 95% CI, 1.34-2.38, P=7.90 × 10(-5); DROSHA r... BeFree 23763827 Detail
<0.001 malignant peripheral nerve sheath tumor Four SNPs (DDX5 rs1991401, OR=1.79, 95% CI, 1.34-2.38, P=7.90 × 10(-5); DROSHA r... BeFree 23763827 Detail
<0.001 malignant peripheral nerve sheath tumor Four SNPs (DDX5 rs1991401, OR=1.79, 95% CI, 1.34-2.38, P=7.90 × 10(-5); DROSHA r... BeFree 23763827 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_015721.3(GEMIN4):c.3097C>T (p.Arg1033Cys) AND not provided ClinVar Detail
NM_015721.3(GEMIN4):c.3097C>T (p.Arg1033Cys) AND Neurodevelopmental disorder with microcephaly, cata... ClinVar Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381... DisGeNET Detail
To explore the relationship between three SNPs (rs3757 in DGCR8, rs636832 in AGO1, rs7813 in GEMIN4)... DisGeNET Detail
Four SNPs (DDX5 rs1991401, OR=1.79, 95% CI, 1.34-2.38, P=7.90 × 10(-5); DROSHA rs10719, OR=1.64, 95%... DisGeNET Detail
Four SNPs (DDX5 rs1991401, OR=1.79, 95% CI, 1.34-2.38, P=7.90 × 10(-5); DROSHA rs10719, OR=1.64, 95%... DisGeNET Detail
Four SNPs (DDX5 rs1991401, OR=1.79, 95% CI, 1.34-2.38, P=7.90 × 10(-5); DROSHA rs10719, OR=1.64, 95%... DisGeNET Detail
Four SNPs (DDX5 rs1991401, OR=1.79, 95% CI, 1.34-2.38, P=7.90 × 10(-5); DROSHA rs10719, OR=1.64, 95%... 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
rs7813 dbSNP
Genome
hg19
Position
chr17:648,186-648,186
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1179
Mean of sample read depth (HGVD)
31.17
Standard deviation of sample read depth (HGVD)
15.43
Number of reference allele (HGVD)
789
Number of alternative allele (HGVD)
1569
Allele Frequency (HGVD)
0.6653944020356234
Gene Symbol (HGVD)
GEMIN4
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))
rs7813
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6595
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11054
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8548
East Asian Allele Counts (ExAC)
5996
East Asian Heterozygous Counts (ExAC)
1782
East Asian Homozygous Counts (ExAC)
2107
East Asian Allele Frequency (ExAC)
0.7014506317267197
Chromosome Counts in All Race (ExAC)
119792
Allele Counts in All Race (ExAC)
74807
Heterozygous Counts in All Race (ExAC)
27215
Homozygous Counts in All Race (ExAC)
23796
Allele Frequency in All Race (ExAC)
0.6244740884199279
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