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NM_000535.7(PMS2):c.2148C>T (p.Thr716=) AND Malignant tumor of breast

Germline classification:
Likely benign (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001357183.3

Allele description [Variation Report for NM_000535.7(PMS2):c.2148C>T (p.Thr716=)]

NM_000535.7(PMS2):c.2148C>T (p.Thr716=)

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.2148C>T (p.Thr716=)
HGVS:
  • NC_000007.14:g.5982850G>A
  • NG_008466.1:g.31257C>T
  • NM_000535.7:c.2148C>TMANE SELECT
  • NM_001322003.2:c.1743C>T
  • NM_001322004.2:c.1743C>T
  • NM_001322005.2:c.1743C>T
  • NM_001322006.2:c.1992C>T
  • NM_001322007.2:c.1830C>T
  • NM_001322008.2:c.1830C>T
  • NM_001322009.2:c.1743C>T
  • NM_001322010.2:c.1587C>T
  • NM_001322011.2:c.1215C>T
  • NM_001322012.2:c.1215C>T
  • NM_001322013.2:c.1575C>T
  • NM_001322014.2:c.2148C>T
  • NM_001322015.2:c.1839C>T
  • NP_000526.2:p.Thr716=
  • NP_001308932.1:p.Thr581=
  • NP_001308933.1:p.Thr581=
  • NP_001308934.1:p.Thr581=
  • NP_001308935.1:p.Thr664=
  • NP_001308936.1:p.Thr610=
  • NP_001308937.1:p.Thr610=
  • NP_001308938.1:p.Thr581=
  • NP_001308939.1:p.Thr529=
  • NP_001308940.1:p.Thr405=
  • NP_001308941.1:p.Thr405=
  • NP_001308942.1:p.Thr525=
  • NP_001308943.1:p.Thr716=
  • NP_001308944.1:p.Thr613=
  • LRG_161t1:c.2148C>T
  • LRG_161:g.31257C>T
  • NC_000007.13:g.6022481G>A
  • NM_000535.5:c.2148C>T
  • NM_000535.6:c.2148C>T
  • NR_136154.1:n.2235C>T
  • p.T716T
Links:
dbSNP: rs748404138
NCBI 1000 Genomes Browser:
rs748404138
Molecular consequence:
  • NR_136154.1:n.2235C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000535.7:c.2148C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322003.2:c.1743C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322004.2:c.1743C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322005.2:c.1743C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322006.2:c.1992C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322007.2:c.1830C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322008.2:c.1830C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322009.2:c.1743C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322010.2:c.1587C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322011.2:c.1215C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322012.2:c.1215C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322013.2:c.1575C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322014.2:c.2148C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322015.2:c.1839C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Malignant tumor of breast
Synonyms:
Malignant breast neoplasm; Cancer breast
Identifiers:
MONDO: MONDO:0007254; MedGen: C0006142

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001552562Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely benignunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001552562.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The PMS2 p.Thr716= variant was not identified in the literature. The variant was identified in dbSNP (ID: rs748404138) as "With Likely benign allele", ClinVar (classified as likely benign by Ambry Genetics and GeneDx).The variant was identified in control databases in 6 of 263760 chromosomes at a frequency of 0.00002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Other in 1 of 6242 chromosomes (freq: 0.00016), European Non-Finnish in 3 of 119500 chromosomes (freq: 0.000025), East Asian in 1 of 18288 chromosomes (freq: 0.000055), and South Asian in 1 of 29828 chromosomes (freq: 0.000034), while the variant was not observed in the African, Latino, Ashkenazi Jewish, or Finnish populations. The PMS2 c.2148C>T variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In addition, the nucleotide at position c.2148 is not highly conserved across mammalian species. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024