chr16:58553833:C>T Detail (hg38) (CNOT1)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
Genome browser

Information

Genome

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

HGVS

CNOT1

Type	Transcript	Protein
RefSeq	NM_001265612.1:c.2919G>A	NP_001252541.1:p.Gln973=
	NM_016284.4:c.2919G>A	NP_057368.3:p.Gln973=
	NM_206999.2:c.2919G>A	NP_996882.1:p.Gln973=
Ensemble	ENST00000317147.10:c.2919G>A	ENST00000317147.10:p.Gln973=
	ENST00000441024.6:c.2919G>A	ENST00000441024.6:p.Gln973=
	ENST00000569240.5:c.2904G>A	ENST00000569240.5:p.Gln968=

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
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Links

CNOT1

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

Descrption	Source	Links
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: hg38
Position: chr16:58,553,833-58,553,833
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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