NM_002691.4(POLD1):c.1665C>T (p.Val555=) AND not specified

Germline classification:: Benign/Likely benign (5 submissions)
Last evaluated:: Aug 15, 2023
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:: RCV000439741.22

Allele description [Variation Report for NM_002691.4(POLD1):c.1665C>T (p.Val555=)]

NM_002691.4(POLD1):c.1665C>T (p.Val555=)

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.1665C>T (p.Val555=)

HGVS:

NC_000019.10:g.50407153C>T
NG_033800.1:g.27831C>T
NM_001256849.1:c.1665C>T
NM_001308632.1:c.1665C>T
NM_002691.4:c.1665C>TMANE SELECT
NP_001243778.1:p.Val555=
NP_001295561.1:p.Val555=
NP_002682.2:p.Val555=
LRG_785t1:c.1665C>T
LRG_785t2:c.1665C>T
LRG_785:g.27831C>T
LRG_785p1:p.Val555=
LRG_785p2:p.Val555=
NC_000019.9:g.50910410C>T
NM_002691.2:c.1665C>T
NM_002691.3:c.1665C>T
NR_046402.2:n.1710C>T
p.Val555Val

Links:

dbSNP: rs150238541

NCBI 1000 Genomes Browser:

rs150238541

Molecular consequence:

NR_046402.2:n.1710C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001256849.1:c.1665C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001308632.1:c.1665C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_002691.4:c.1665C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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Homo sapiens trafficking protein particle complex 10, mRNA (cDNA clone MGC:12677...
Homo sapiens trafficking protein particle complex 10, mRNA (cDNA clone MGC:126777 IMAGE:8069234), complete cds
gi|75516746|gb|BC101728.1|

Nucleotide
Homo sapiens WD repeat domain 22, mRNA (cDNA clone MGC:168245 IMAGE:9020622), co...
Homo sapiens WD repeat domain 22, mRNA (cDNA clone MGC:168245 IMAGE:9020622), complete cds
gi|187956706|gb|BC136632.1|

Nucleotide
Homo sapiens cDNA FLJ36964 fis, clone BRACE2006072
Homo sapiens cDNA FLJ36964 fis, clone BRACE2006072
gi|21753311|dbj|AK094283.1|

Nucleotide
INPP1 inositol polyphosphate-1-phosphatase [Homo sapiens]
INPP1 inositol polyphosphate-1-phosphatase [Homo sapiens]
Gene ID:3628

Gene
Gene Links for GEO Profiles (Select 130959075) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000520753	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely benign (Dec 28, 2017)	germline	clinical testing	Citation Link,
SCV000806472	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jan 30, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001159617	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Benign (Apr 30, 2019)	germline	clinical testing	Citation Link,
SCV002065991	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jan 7, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002551921	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Aug 15, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

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 GeneDx, SCV000520753.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000806472.1

#	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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001159617.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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 Genetic Services Laboratory, University of Chicago, SCV002065991.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, SCV002551921.4

#	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: Oct 20, 2024

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