chr2:189784590:G>C Detail (hg38) (PMS1)

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

Information

Genome

Assembly	Position
hg19	chr2:190,649,316-190,649,316 View the variant detail on this assembly version.
hg38	chr2:189,784,590-189,784,590

HGVS

PMS1

Type	Transcript	Protein
RefSeq	NM_001321051.1:c.-24G>C
	NM_001128143.1:c.-24G>C
	NM_001321049.1:c.-24G>C
	NM_001289409.1:c.-266G>C
	NM_000534.4:c.-24G>C
	NM_001321045.1:c.-24G>C
	NM_001321046.1:c.-24G>C
	NM_001321047.1:c.-24G>C
	NM_001321048.1:c.-24G>C
	NM_001128144.1:c.-24G>C
	NM_001321044.1:c.-24G>C
	NM_001289408.1:c.-449G>C
Ensemble	ENST00000374826.8:c.-24G>C
	ENST00000409823.7:c.-24G>C
	ENST00000409985.5:c.-24G>C
	ENST00000418224.7:c.-24G>C
	ENST00000432292.7:c.-266G>C
	ENST00000441310.7:c.-24G>C
	ENST00000447232.6:c.-24G>C
	ENST00000618056.4:c.-24G>C
	ENST00000624204.3:c.-449G>C

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:[No Data.]
	ToMMo:0.240
	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

PMS1

Type	Database	ID	Link
Gene	MIM	600258	OMIM
	HGNC	9121	HGNC
	Ensembl	ENSG00000064933	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv9903590	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2015-03-03	criteria provided, single submitter	not provided	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.005	Carcinoma of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail
0.021	Malignant neoplasm of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail
0.020	Carcinoma of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail
<0.001	Carcinoma of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail
<0.001	Carcinoma of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail
0.214	Malignant neoplasm of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail
0.100	Malignant neoplasm of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail
<0.001	Carcinoma of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail
0.010	Malignant neoplasm of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail
0.003	Malignant neoplasm of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail
0.014	Carcinoma of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail
<0.001	Malignant neoplasm of lung	SNPs associated with lung cancer prognosis primarily mapped to 14 genes in diffe...	BeFree	21739480	Detail

Annotation

Annotations

Descrption	Source	Links
NM_000534.5(PMS1):c.-24G>C AND not provided	ClinVar	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	DisGeNET	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	DisGeNET	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	DisGeNET	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	DisGeNET	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	DisGeNET	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	DisGeNET	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	DisGeNET	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	DisGeNET	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	DisGeNET	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	DisGeNET	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	DisGeNET	Detail
SNPs associated with lung cancer prognosis primarily mapped to 14 genes in different repair pathways...	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: rs5742933 dbSNP
Genome: hg38
Position: chr2:189,784,590-189,784,590
Variant Type: snv
Reference Allele: G
Alternative Allele: C
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)): rs5742933
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.2398
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 4019
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760

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