chr16:58587737:C>T Detail (hg19) (CNOT1)

Information

Genome

Assembly Position
hg19 chr16:58,587,737-58,587,737
hg38 chr16:58,553,833-58,553,833 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_206999.2:c.2919G>A NP_996882.1:p.Gln973=
NM_001265612.1:c.2919G>A NP_001252541.1:p.Gln973=
NM_016284.4:c.2919G>A NP_057368.3:p.Gln973=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.628
ToMMo:0.641
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.587

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 604917 OMIM
HGNC 7877 HGNC
Ensembl ENSG00000125107 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv55679031 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-07-22 criteria provided, single submitter Holoprosencephaly 12 with or without pancreatic agenesis germline Detail
Benign 2021-07-22 criteria provided, single submitter Vissers-Bodmer syndrome germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2019-10-18 criteria provided, single submitter CNOT1-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Osteosarcoma of bone This study suggests that SNPs in RISC complex genes may be involved in osteosarc... BeFree 25663449 Detail
<0.001 osteosarcoma This study suggests that SNPs in RISC complex genes may be involved in osteosarc... BeFree 25663449 Detail
<0.001 osteosarcoma This study suggests that SNPs in RISC complex genes may be involved in osteosarc... BeFree 25663449 Detail
<0.001 Osteosarcoma of bone This study suggests that SNPs in RISC complex genes may be involved in osteosarc... BeFree 25663449 Detail
<0.001 chronic lymphocytic leukemia We found nine statistically significant associations with CLL risk after FDR cor... BeFree 25793711 Detail
<0.001 chronic lymphocytic leukemia We found nine statistically significant associations with CLL risk after FDR cor... BeFree 25793711 Detail
<0.001 chronic lymphocytic leukemia We found nine statistically significant associations with CLL risk after FDR cor... BeFree 25793711 Detail
<0.001 chronic lymphocytic leukemia We found nine statistically significant associations with CLL risk after FDR cor... BeFree 25793711 Detail
<0.001 chronic lymphocytic leukemia We found nine statistically significant associations with CLL risk after FDR cor... BeFree 25793711 Detail
<0.001 chronic lymphocytic leukemia We found nine statistically significant associations with CLL risk after FDR cor... BeFree 25793711 Detail
<0.001 chronic lymphocytic leukemia We found nine statistically significant associations with CLL risk after FDR cor... BeFree 25793711 Detail
<0.001 chronic lymphocytic leukemia We found nine statistically significant associations with CLL risk after FDR cor... BeFree 25793711 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_016284.5(CNOT1):c.2919G>A (p.Gln973=) AND Holoprosencephaly 12 with or without pancreatic agenesi... ClinVar Detail
NM_016284.5(CNOT1):c.2919G>A (p.Gln973=) AND Vissers-Bodmer syndrome ClinVar Detail
NM_016284.5(CNOT1):c.2919G>A (p.Gln973=) AND not provided ClinVar Detail
NM_016284.5(CNOT1):c.2919G>A (p.Gln973=) AND CNOT1-related disorder ClinVar Detail
This study suggests that SNPs in RISC complex genes may be involved in osteosarcoma susceptibility, ... DisGeNET Detail
This study suggests that SNPs in RISC complex genes may be involved in osteosarcoma susceptibility, ... DisGeNET Detail
This study suggests that SNPs in RISC complex genes may be involved in osteosarcoma susceptibility, ... DisGeNET Detail
This study suggests that SNPs in RISC complex genes may be involved in osteosarcoma susceptibility, ... DisGeNET Detail
We found nine statistically significant associations with CLL risk after FDR correction, seven in mi... DisGeNET Detail
We found nine statistically significant associations with CLL risk after FDR correction, seven in mi... DisGeNET Detail
We found nine statistically significant associations with CLL risk after FDR correction, seven in mi... DisGeNET Detail
We found nine statistically significant associations with CLL risk after FDR correction, seven in mi... DisGeNET Detail
We found nine statistically significant associations with CLL risk after FDR correction, seven in mi... DisGeNET Detail
We found nine statistically significant associations with CLL risk after FDR correction, seven in mi... DisGeNET Detail
We found nine statistically significant associations with CLL risk after FDR correction, seven in mi... DisGeNET Detail
We found nine statistically significant associations with CLL risk after FDR correction, seven in mi... 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
rs11866002 dbSNP
Genome
hg19
Position
chr16:58,587,737-58,587,737
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1205
Mean of sample read depth (HGVD)
83.83
Standard deviation of sample read depth (HGVD)
41.38
Number of reference allele (HGVD)
896
Number of alternative allele (HGVD)
1512
Allele Frequency (HGVD)
0.627906976744186
Gene Symbol (HGVD)
CNOT1
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))
rs11866002
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6415
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10751
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8630
East Asian Allele Counts (ExAC)
5062
East Asian Heterozygous Counts (ExAC)
2078
East Asian Homozygous Counts (ExAC)
1492
East Asian Allele Frequency (ExAC)
0.586558516801854
Chromosome Counts in All Race (ExAC)
121320
Allele Counts in All Race (ExAC)
44687
Heterozygous Counts in All Race (ExAC)
26575
Homozygous Counts in All Race (ExAC)
9056
Allele Frequency in All Race (ExAC)
0.36833992746455657
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