chr7:5987328:G>C Detail (hg38) (PMS2)

Information

Genome

Assembly Position
hg19 chr7:6,026,959-6,026,959 View the variant detail on this assembly version.
hg38 chr7:5,987,328-5,987,328

HGVS

Type Transcript Protein
RefSeq NM_000535.6:c.1437C>G NP_000526.2:p.His479Gln
NM_001322006.1:c.1437C>G NP_001308935.1:p.His479Gln
NM_001322014.1:c.1437C>G NP_001308943.1:p.His479Gln
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
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 tgv28188279 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2024-04-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Uncertain significance 2015-11-20 criteria provided, single submitter Lynch syndrome germline Detail
Benign Likely benign 2023-08-15 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2020-08-18 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign Likely benign 2019-05-28 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
Benign no assertion criteria provided unknown Detail
Benign 2021-06-08 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
Benign 2022-01-01 criteria provided, single submitter ovarian cancer germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000535.7(PMS2):c.1437C>G (p.His479Gln) AND not provided ClinVar Detail
NM_000535.7(PMS2):c.1437C>G (p.His479Gln) AND Lynch syndrome ClinVar Detail
NM_000535.7(PMS2):c.1437C>G (p.His479Gln) AND not specified ClinVar Detail
NM_000535.7(PMS2):c.1437C>G (p.His479Gln) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000535.7(PMS2):c.1437C>G (p.His479Gln) AND Lynch syndrome 4 ClinVar Detail
NM_000535.7(PMS2):c.1437C>G (p.His479Gln) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000535.7(PMS2):c.1437C>G (p.His479Gln) AND Malignant tumor of breast ClinVar Detail
NM_000535.7(PMS2):c.1437C>G (p.His479Gln) AND Breast and/or ovarian cancer ClinVar Detail
NM_000535.7(PMS2):c.1437C>G (p.His479Gln) AND Ovarian cancer ClinVar 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
rs63750685 dbSNP
Genome
hg38
Position
chr7:5,987,328-5,987,328
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
67.12
Standard deviation of sample read depth (HGVD)
34.73
Number of reference allele (HGVD)
2417
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1356492969396195E-4
Gene Symbol (HGVD)
PMS2
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
VQSRTrancheSNP99.80to99.90
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs63750685
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
7
East Asian Heterozygous Counts (ExAC)
7
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
8.088745088976196E-4
Chromosome Counts in All Race (ExAC)
121410
Allele Counts in All Race (ExAC)
552
Heterozygous Counts in All Race (ExAC)
546
Homozygous Counts in All Race (ExAC)
3
Allele Frequency in All Race (ExAC)
0.004546577711885347
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