chr7:6038722:T>C Detail (hg19) (PMS2)

Information

Genome

Assembly Position
hg19 chr7:6,038,722-6,038,722
hg38 chr7:5,999,091-5,999,091 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000535.6:c.705+17A>G
NM_001322006.1:c.705+17A>G
NM_001322014.1:c.705+17A>G
Summary

MGeND

Clinical significance Benign
Variant entry 3,524
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.394
ToMMo:0.378
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.366

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600259 OMIM
HGNC 9122 HGNC
Ensembl ENSG00000122512 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv28189248 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign 2020/04/20 cervical part of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 abdominal part of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 upper third of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 middle third of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 lower third of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 oesophagus, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 fundus of stomach not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 body of stomach not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 pyloric antrum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 stomach, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 duodenum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 jejunum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ileum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 small intestine, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 caecum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 appendix not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ascending colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 transverse colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 descending colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 sigmoid colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 colon, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of rectosigmoid junction not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of rectum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 anal canal not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 liver cell carcinoma not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 intrahepatic bile duct carcinoma not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of gallbladder not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 extrahepatic bile duct not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ampulla of vater not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 head of pancreas not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 body of pancreas not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 tail of pancreas not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ill-defined sites within the digestive system not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 bronchus or lung, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 retroperitoneum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2013-09-05 reviewed by expert panel Lynch syndrome germline not provided Detail
Benign 2013-08-22 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign 2015-03-31 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2023-07-07 criteria provided, multiple submitters, no conflicts Lynch syndrome 4 germline Detail
Benign 2024-02-01 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Benign 2023-11-29 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2021-10-25 criteria provided, single submitter Mismatch repair cancer syndrome 4 germline Detail
Benign 2021-04-21 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000535.7(PMS2):c.705+17A>G AND Lynch syndrome ClinVar Detail
NM_000535.7(PMS2):c.705+17A>G AND not specified ClinVar Detail
NM_000535.7(PMS2):c.705+17A>G AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000535.7(PMS2):c.705+17A>G AND Lynch syndrome 4 ClinVar Detail
NM_000535.7(PMS2):c.705+17A>G AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000535.7(PMS2):c.705+17A>G AND not provided ClinVar Detail
NM_000535.7(PMS2):c.705+17A>G AND Mismatch repair cancer syndrome 4 ClinVar Detail
NM_000535.7(PMS2):c.705+17A>G AND Breast and/or ovarian cancer ClinVar Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs62456182 dbSNP
Genome
hg19
Position
chr7:6,038,722-6,038,722
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
834
Mean of sample read depth (HGVD)
35.33
Standard deviation of sample read depth (HGVD)
14.16
Number of reference allele (HGVD)
1010
Number of alternative allele (HGVD)
658
Allele Frequency (HGVD)
0.39448441247002397
Gene Symbol (HGVD)
PMS2
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))
rs62456182
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.378
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6334
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8640
East Asian Allele Counts (ExAC)
3158
East Asian Heterozygous Counts (ExAC)
2008
East Asian Homozygous Counts (ExAC)
575
East Asian Allele Frequency (ExAC)
0.36550925925925926
Chromosome Counts in All Race (ExAC)
121368
Allele Counts in All Race (ExAC)
44634
Heterozygous Counts in All Race (ExAC)
27612
Homozygous Counts in All Race (ExAC)
8511
Allele Frequency in All Race (ExAC)
0.36775756377298796
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