chr7:5977709:T>C Detail (hg38) (PMS2)

Information

Genome

Assembly Position
hg19 chr7:6,017,340-6,017,340 View the variant detail on this assembly version.
hg38 chr7:5,977,709-5,977,709

HGVS

Type Transcript Protein
RefSeq NM_000535.6:c.2324A>G NP_000526.2:p.Asn775Ser
NM_001322006.1:c.2324A>G NP_001308935.1:p.Asn775Ser
NM_001322014.1:c.2324A>G NP_001308943.1:p.Asn775Ser
Summary

MGeND

Clinical significance Likely benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

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 tgv28187558 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Likely benign 2023/02/27 ascending colon germline MGS000029
(TMGS000133) 		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 unknown Detail
Benign 2023-08-15 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign Likely benign 2021-04-27 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2014-07-24 no assertion criteria provided Lynch syndrome 1 germline Detail
Benign 2023-05-11 criteria provided, multiple submitters, no conflicts Lynch syndrome 4 germline unknown Detail
Benign 2024-02-01 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Likely benign 2018-10-31 criteria provided, single submitter Lynch syndrome 4,Mismatch repair cancer syndrome 1 unknown Detail
Likely benign 2018-10-31 criteria provided, single submitter Lynch syndrome 4,Mismatch repair cancer syndrome 1 unknown Detail
Benign no assertion criteria provided endometrial carcinoma unknown Detail
Benign Likely benign 2023-10-23 criteria provided, multiple submitters, no conflicts not provided germline Detail
Likely benign 2022-09-13 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 oligospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
<0.001 azoospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
0.005 azoospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
0.003 oligospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
<0.001 azoospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
<0.001 oligospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) AND Lynch syndrome ClinVar Detail
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) AND not specified ClinVar Detail
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) AND Lynch syndrome 1 ClinVar Detail
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) AND Lynch syndrome 4 ClinVar Detail
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) AND multiple conditions ClinVar Detail
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) AND multiple conditions ClinVar Detail
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) AND Endometrial carcinoma ClinVar Detail
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) AND not provided ClinVar Detail
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) AND Breast and/or ovarian cancer ClinVar Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... DisGeNET Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... DisGeNET Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... DisGeNET Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... DisGeNET Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... DisGeNET Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... 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
rs17420802 dbSNP
Genome
hg38
Position
chr7:5,977,709-5,977,709
Variant Type
snv
Reference Allele
T
Alternative Allele
C
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
VQSRTrancheSNP99.60to99.80
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs17420802
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0003
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16692
East Asian Chromosome Counts (ExAC)
8616
East Asian Allele Counts (ExAC)
3
East Asian Heterozygous Counts (ExAC)
3
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
3.4818941504178273E-4
Chromosome Counts in All Race (ExAC)
120648
Allele Counts in All Race (ExAC)
45
Heterozygous Counts in All Race (ExAC)
43
Homozygous Counts in All Race (ExAC)
1
Allele Frequency in All Race (ExAC)
3.72985876268152E-4
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