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NM_002691.4(POLD1):c.13C>T (p.Arg5Trp) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Nov 11, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV002257545.3

Allele description [Variation Report for NM_002691.4(POLD1):c.13C>T (p.Arg5Trp)]

NM_002691.4(POLD1):c.13C>T (p.Arg5Trp)

Gene:
POLD1:DNA polymerase delta 1, catalytic subunit [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.33
Genomic location:
Preferred name:
NM_002691.4(POLD1):c.13C>T (p.Arg5Trp)
HGVS:
  • NC_000019.10:g.50398864C>T
  • NG_033800.1:g.19542C>T
  • NM_001256849.1:c.13C>T
  • NM_001308632.1:c.13C>T
  • NM_002691.2:c.13C>T
  • NM_002691.4:c.13C>TMANE SELECT
  • NP_001243778.1:p.Arg5Trp
  • NP_001295561.1:p.Arg5Trp
  • NP_002682.2:p.Arg5Trp
  • LRG_785t1:c.13C>T
  • LRG_785t2:c.13C>T
  • LRG_785:g.19542C>T
  • LRG_785p1:p.Arg5Trp
  • LRG_785p2:p.Arg5Trp
  • NC_000019.9:g.50902121C>T
  • NM_002691.3:c.13C>T
  • NR_046402.2:n.58C>T
  • P28340:p.Arg5Trp
Protein change:
R5W
Links:
UniProtKB: P28340#VAR_048878; dbSNP: rs9282830
NCBI 1000 Genomes Browser:
rs9282830
Molecular consequence:
  • NM_001256849.1:c.13C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001308632.1:c.13C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002691.4:c.13C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_046402.2:n.58C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002534582Sema4, Sema4
criteria provided, single submitter

(Sema4 Curation Guidelines)
Likely benign
(Oct 9, 2020)
germlinecuration

Citation Link,

SCV003909062Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Likely benign
(Nov 11, 2022)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation

Details of each submission

From Sema4, Sema4, SCV002534582.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Ambry Genetics, SCV003909062.2

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

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

Last Updated: Jul 15, 2024