NM_000535.7(PMS2):c.2088C>T (p.Phe696=) AND Hereditary cancer-predisposing syndrome
- Germline classification:
- Likely benign (2 submissions)
- Last evaluated:
- Dec 14, 2021
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV002423982.3
Allele description [Variation Report for NM_000535.7(PMS2):c.2088C>T (p.Phe696=)]
NM_000535.7(PMS2):c.2088C>T (p.Phe696=)
- Gene:
- PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 7p22.1
- Genomic location:
- Preferred name:
- NM_000535.7(PMS2):c.2088C>T (p.Phe696=)
- HGVS:
- NC_000007.14:g.5982910G>A
- NG_008466.1:g.31197C>T
- NM_000535.7:c.2088C>TMANE SELECT
- NM_001018040.1:c.1683C>T
- NM_001322003.2:c.1683C>T
- NM_001322004.2:c.1683C>T
- NM_001322005.2:c.1683C>T
- NM_001322006.2:c.1932C>T
- NM_001322007.2:c.1770C>T
- NM_001322008.2:c.1770C>T
- NM_001322009.2:c.1683C>T
- NM_001322010.2:c.1527C>T
- NM_001322011.2:c.1155C>T
- NM_001322012.2:c.1155C>T
- NM_001322013.2:c.1515C>T
- NM_001322014.2:c.2088C>T
- NM_001322015.2:c.1779C>T
- NM_001406866.1:c.2274C>T
- NM_001406868.1:c.2112C>T
- NM_001406869.1:c.1980C>T
- NM_001406870.1:c.1932C>T
- NM_001406871.1:c.2088C>T
- NM_001406872.1:c.2006+3849C>T
- NM_001406873.1:c.1890C>T
- NM_001406874.1:c.1920C>T
- NM_001406875.1:c.1779C>T
- NM_001406876.1:c.1770C>T
- NM_001406877.1:c.1779C>T
- NM_001406878.1:c.1779C>T
- NM_001406879.1:c.1779C>T
- NM_001406880.1:c.1779C>T
- NM_001406881.1:c.1779C>T
- NM_001406882.1:c.1779C>T
- NM_001406883.1:c.1770C>T
- NM_001406884.1:c.1764C>T
- NM_001406885.1:c.1752C>T
- NM_001406886.1:c.1722C>T
- NM_001406887.1:c.1683C>T
- NM_001406888.1:c.1683C>T
- NM_001406889.1:c.1683C>T
- NM_001406890.1:c.1683C>T
- NM_001406891.1:c.1683C>T
- NM_001406892.1:c.1683C>T
- NM_001406893.1:c.1683C>T
- NM_001406894.1:c.1683C>T
- NM_001406895.1:c.1683C>T
- NM_001406896.1:c.1683C>T
- NM_001406897.1:c.1683C>T
- NM_001406898.1:c.1683C>T
- NM_001406899.1:c.1683C>T
- NM_001406900.1:c.1623C>T
- NM_001406901.1:c.1614C>T
- NM_001406902.1:c.1614C>T
- NM_001406903.1:c.1688+3849C>T
- NM_001406904.1:c.1575C>T
- NM_001406905.1:c.1575C>T
- NM_001406906.1:c.1527C>T
- NM_001406907.1:c.1527C>T
- NM_001406908.1:c.1601+3849C>T
- NM_001406909.1:c.1515C>T
- NM_001406910.1:c.1601+3849C>T
- NM_001406911.1:c.1317C>T
- NM_001406912.1:c.885C>T
- NP_000526.1:p.Phe696=
- NP_000526.2:p.Phe696=
- NP_001018050.1:p.Phe561=
- NP_001308932.1:p.Phe561=
- NP_001308933.1:p.Phe561=
- NP_001308934.1:p.Phe561=
- NP_001308935.1:p.Phe644=
- NP_001308936.1:p.Phe590=
- NP_001308937.1:p.Phe590=
- NP_001308938.1:p.Phe561=
- NP_001308939.1:p.Phe509=
- NP_001308940.1:p.Phe385=
- NP_001308941.1:p.Phe385=
- NP_001308942.1:p.Phe505=
- NP_001308943.1:p.Phe696=
- NP_001308944.1:p.Phe593=
- NP_001393795.1:p.Phe758=
- NP_001393797.1:p.Phe704=
- NP_001393798.1:p.Phe660=
- NP_001393799.1:p.Phe644=
- NP_001393800.1:p.Phe696=
- NP_001393802.1:p.Phe630=
- NP_001393803.1:p.Phe640=
- NP_001393804.1:p.Phe593=
- NP_001393805.1:p.Phe590=
- NP_001393806.1:p.Phe593=
- NP_001393807.1:p.Phe593=
- NP_001393808.1:p.Phe593=
- NP_001393809.1:p.Phe593=
- NP_001393810.1:p.Phe593=
- NP_001393811.1:p.Phe593=
- NP_001393812.1:p.Phe590=
- NP_001393813.1:p.Phe588=
- NP_001393814.1:p.Phe584=
- NP_001393815.1:p.Phe574=
- NP_001393816.1:p.Phe561=
- NP_001393817.1:p.Phe561=
- NP_001393818.1:p.Phe561=
- NP_001393819.1:p.Phe561=
- NP_001393820.1:p.Phe561=
- NP_001393821.1:p.Phe561=
- NP_001393822.1:p.Phe561=
- NP_001393823.1:p.Phe561=
- NP_001393824.1:p.Phe561=
- NP_001393825.1:p.Phe561=
- NP_001393826.1:p.Phe561=
- NP_001393827.1:p.Phe561=
- NP_001393828.1:p.Phe561=
- NP_001393829.1:p.Phe541=
- NP_001393830.1:p.Phe538=
- NP_001393831.1:p.Phe538=
- NP_001393833.1:p.Phe525=
- NP_001393834.1:p.Phe525=
- NP_001393835.1:p.Phe509=
- NP_001393836.1:p.Phe509=
- NP_001393838.1:p.Phe505=
- NP_001393840.1:p.Phe439=
- NP_001393841.1:p.Phe295=
- LRG_161t1:c.2088C>T
- LRG_161:g.31197C>T
- LRG_161p1:p.Phe696=
- NC_000007.13:g.6022541G>A
- NM_000535.5:c.2088C>T
- NR_003085.2:n.2170C>T
- NR_136154.1:n.2175C>T
This HGVS expression did not pass validation- Molecular consequence:
- NM_001406872.1:c.2006+3849C>T - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406903.1:c.1688+3849C>T - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406908.1:c.1601+3849C>T - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406910.1:c.1601+3849C>T - intron variant - [Sequence Ontology: SO:0001627]
- NR_136154.1:n.2175C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NM_000535.7:c.2088C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001018040.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322003.2:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322004.2:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322005.2:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322006.2:c.1932C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322007.2:c.1770C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322008.2:c.1770C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322009.2:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322010.2:c.1527C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322011.2:c.1155C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322012.2:c.1155C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322013.2:c.1515C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322014.2:c.2088C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322015.2:c.1779C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406866.1:c.2274C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406868.1:c.2112C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406869.1:c.1980C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406870.1:c.1932C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406871.1:c.2088C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406873.1:c.1890C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406874.1:c.1920C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406875.1:c.1779C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406876.1:c.1770C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406877.1:c.1779C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406878.1:c.1779C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406879.1:c.1779C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406880.1:c.1779C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406881.1:c.1779C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406882.1:c.1779C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406883.1:c.1770C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406884.1:c.1764C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406885.1:c.1752C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406886.1:c.1722C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406887.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406888.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406889.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406890.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406891.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406892.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406893.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406894.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406895.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406896.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406897.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406898.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406899.1:c.1683C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406900.1:c.1623C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406901.1:c.1614C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406902.1:c.1614C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406904.1:c.1575C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406905.1:c.1575C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406906.1:c.1527C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406907.1:c.1527C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406909.1:c.1515C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406911.1:c.1317C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406912.1:c.885C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Condition(s)
- Name:
- Hereditary cancer-predisposing syndrome
- Synonyms:
- Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
- Identifiers:
- MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV002727831 | Ambry Genetics | criteria provided, single submitter (Ambry Variant Classification Scheme 2023) | Likely benign (Nov 14, 2019) | germline | clinical testing | |
SCV004359558 | Color Diagnostics, LLC DBA Color Health | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely benign (Dec 14, 2021) | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
Citations
PubMed
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..
Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.
PubMed [citation]
- PMID:
- 25741868
- PMCID:
- PMC4544753
Details of each submission
From Ambry Genetics, SCV002727831.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
Description
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Color Diagnostics, LLC DBA Color Health, SCV004359558.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
Last Updated: May 1, 2024