chr1:45797760:T>C Detail (hg19) (MUTYH)

Information

Genome

Assembly Position
hg19 chr1:45,797,760-45,797,760
hg38 chr1:45,332,088-45,332,088 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001293195.1:c.850-2A>G
NM_001048172.1:c.850-2A>G
NM_001048173.1:c.850-2A>G
Summary

MGeND

Clinical significance Likely pathogenic Pathogenic Uncertain significance
Variant entry 28
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.025
ToMMo:0.021
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.014

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 604933 OMIM
HGNC 7527 HGNC
Ensembl ENSG00000132781 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv1349363 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Uncertain significance 2018/05/08 other germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Likely pathogenic 2018/12/08 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Likely pathogenic 2018/12/09 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Likely pathogenic 2019/09/20 malignant neoplasm of rectum germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2018/04/27 malignant neoplasm of thyroid gland germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/05/08 malignant neoplasm of rectum germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/10/08 extrahepatic bile ducts germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Likely pathogenic 2018/12/09 other germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2018/04/27 ascending colon germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/05/08 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/06/24 bone and articular cartilage, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/10/08 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/06/24 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/10/20 polyp of stomach and duodenum germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/06/24 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/10/08 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Likely pathogenic 2019/04/23 breast, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2018/04/27 malignant neoplasm of rectum germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/10/20 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/10/20 other germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/10/08 polyp of stomach and duodenum germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/06/24 other germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/05/08 extrahepatic bile ducts germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/05/08 connective and other soft tissue germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2018/10/20 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Likely pathogenic 2019/04/23 carcinoma in situ of breast, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Likely pathogenic other germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2024-02-01 criteria provided, conflicting interpretations familial adenomatous polyposis 2 germline unknown Detail
Conflicting interpretations of pathogenicity 2023-08-28 criteria provided, conflicting interpretations not specified germline Detail
Likely benign 2022-11-14 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Conflicting interpretations of pathogenicity 2023-04-18 criteria provided, conflicting interpretations not provided germline unknown Detail
Likely pathogenic 2018-11-03 criteria provided, single submitter Gastric cancer maternal Detail
Likely pathogenic no assertion criteria provided Carcinoma of colon unknown Detail
Uncertain significance 2024-03-01 criteria provided, single submitter MUTYH-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.120 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
0.480 Colorectal Adenomatous Polyposis, Autosomal Recessive NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001048174.2(MUTYH):c.850-2A>G AND Familial adenomatous polyposis 2 ClinVar Detail
NM_001048174.2(MUTYH):c.850-2A>G AND not specified ClinVar Detail
NM_001048174.2(MUTYH):c.850-2A>G AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_001048174.2(MUTYH):c.850-2A>G AND not provided ClinVar Detail
NM_001048174.2(MUTYH):c.850-2A>G AND Gastric cancer ClinVar Detail
NM_001048174.2(MUTYH):c.850-2A>G AND Carcinoma of colon ClinVar Detail
NM_001048174.2(MUTYH):c.850-2A>G AND MUTYH-related disorder ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs77542170 dbSNP
Genome
hg19
Position
chr1:45,797,760-45,797,760
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
100.10
Standard deviation of sample read depth (HGVD)
46.90
Number of reference allele (HGVD)
2358
Number of alternative allele (HGVD)
60
Allele Frequency (HGVD)
0.02481389578163772
Gene Symbol (HGVD)
MUTYH
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))
rs77542170
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0205
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
343
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8644
East Asian Allele Counts (ExAC)
122
East Asian Heterozygous Counts (ExAC)
120
East Asian Homozygous Counts (ExAC)
1
East Asian Allele Frequency (ExAC)
0.014113836186950486
Chromosome Counts in All Race (ExAC)
121300
Allele Counts in All Race (ExAC)
124
Heterozygous Counts in All Race (ExAC)
122
Homozygous Counts in All Race (ExAC)
1
Allele Frequency in All Race (ExAC)
0.0010222588623248145
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