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NM_002691.4(POLD1):c.1539G>A (p.Leu513=) AND Carcinoma of colon

Germline classification:
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:
RCV001358127.3

Allele description [Variation Report for NM_002691.4(POLD1):c.1539G>A (p.Leu513=)]

NM_002691.4(POLD1):c.1539G>A (p.Leu513=)

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.1539G>A (p.Leu513=)
HGVS:
  • NC_000019.10:g.50407027G>A
  • NG_033800.1:g.27705G>A
  • NM_001256849.1:c.1539G>A
  • NM_001308632.1:c.1539G>A
  • NM_002691.4:c.1539G>AMANE SELECT
  • NP_001243778.1:p.Leu513=
  • NP_001295561.1:p.Leu513=
  • NP_002682.2:p.Leu513=
  • LRG_785t1:c.1539G>A
  • LRG_785t2:c.1539G>A
  • LRG_785:g.27705G>A
  • LRG_785p1:p.Leu513=
  • LRG_785p2:p.Leu513=
  • NC_000019.9:g.50910284G>A
  • NM_001256849.1:c.1539G>A
  • NM_002691.2:c.1539G>A
  • NM_002691.3:c.1539G>A
  • NR_046402.2:n.1584G>A
  • p.Leu513Leu
Links:
dbSNP: rs2230246
NCBI 1000 Genomes Browser:
rs2230246
Molecular consequence:
  • NR_046402.2:n.1584G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001256849.1:c.1539G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001308632.1:c.1539G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_002691.4:c.1539G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Carcinoma of colon (CRC)
Synonyms:
Colonic carcinoma; Colon carcinoma
Identifiers:
MONDO: MONDO:0002032; MedGen: C0699790

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001553782Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
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), SCV001553782.1

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

Description

The POLD1 p.Leu513= variant was identified in dbSNP (ID: rs2230246) “With Benign allele”, and in control databases in 3896 (256 homozygous) of 276006 chromosomes at a frequency of 0.01 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include African in 3409 (250 homozygous) of 23968 chromosomes (freq: 0.14), Other in 42 of 6446 chromosomes (freq: 0.007), Latino in 328 (5 homozygous) of 34406 chromosomes (freq: 0.01), European Non-Finnish in 76 (1 homozygous) of 125746 chromosomes (freq: 0.0006), Ashkenazi Jewish in 32 of 10128 chromosomes (freq: 0.003), and South Asian in 9 of 30774 chromosomes (freq: 0.0003), while not observed in the East Asian and European Finnish populations. The p.Leu513= 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. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.

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

Last Updated: Jun 23, 2024