VCV000259990.34 - ClinVar

NM_006502.3(POLH):c.626G>T (p.Gly209Val)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(14)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Benign/Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_006502.3(POLH):c.626G>T (p.Gly209Val)

Variation ID: 259990 Accession: VCV000259990.34

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 6p21.1 6: 43597831 (GRCh38) [ NCBI UCSC ] 6: 43565568 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 3, 2016	Oct 20, 2024	Apr 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_006502.3:c.626G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_006493.1:p.Gly209Val	missense
NM_001291969.2:c.254G>T	NP_001278898.1:p.Gly85Val	missense
NM_001291970.2:c.626G>T	NP_001278899.1:p.Gly209Val	missense
NC_000006.12:g.43597831G>T
NC_000006.11:g.43565568G>T
NG_009252.1:g.26691G>T
NG_028283.4:g.85744G>T
LRG_470:g.26691G>T
LRG_470t1:c.626G>T	LRG_470p1:p.Gly209Val
	Q9Y253:p.Gly209Val

... more HGVS ... less HGVS

Protein change

G209V, G85V

Other names

Canonical SPDI

NC_000006.12:43597830:G:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.00419 (T)

Allele frequency Help The frequency of the allele represented by this VCV record.

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00223

Trans-Omics for Precision Medicine (TOPMed) 0.00224

The Genome Aggregation Database (gnomAD) 0.00253

Exome Aggregation Consortium (ExAC) 0.00341

The Genome Aggregation Database (gnomAD), exomes 0.00378

1000 Genomes Project 30x 0.00406

1000 Genomes Project 0.00419

Links

ClinGen: CA3827028 UniProtKB: Q9Y253#VAR_021229 dbSNP: rs2307456 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
POLH		-	-	GRCh38 GRCh37	472	579

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not specified	Benign (3)	criteria provided, multiple submitters, no conflicts	Jul 13, 2022	RCV000241818.15
Xeroderma pigmentosum variant type	Benign/Likely benign (5)	criteria provided, multiple submitters, no conflicts	Jul 7, 2023	RCV000615798.17
not provided	Benign/Likely benign (4)	criteria provided, multiple submitters, no conflicts	Apr 1, 2024	RCV000953963.29
Malignant tumor of breast	Benign (1)	no assertion criteria provided	-	RCV001269501.9
Xeroderma pigmentosum	Benign (1)	criteria provided, single submitter	Feb 18, 2021	RCV002257621.8

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Benign (Jul 07, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Xeroderma pigmentosum variant type Affected status: yes Allele origin: germline	KCCC/NGS Laboratory, Kuwait Cancer Control Center Accession: SCV004017094.1 First in ClinVar: Jul 29, 2023 Last updated: Jul 29, 2023
Likely benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005223859.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	NOT SPECIFIED Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV000311510.1 First in ClinVar: Oct 03, 2016 Last updated: Oct 03, 2016
Likely benign (May 28, 2019)	criteria provided, single submitter (Mendelics Assertion Criteria 2017) Method: clinical testing	Xeroderma pigmentosum variant type Affected status: unknown Allele origin: unknown	Mendelics Accession: SCV001137126.1 First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020
Likely benign (Jan 12, 2018)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Xeroderma pigmentosum variant type Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV001321149.1 First in ClinVar: May 31, 2020 Last updated: May 31, 2020	Comment: This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more) This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. (less)
Likely benign (May 06, 2019)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001826732.1 First in ClinVar: Sep 08, 2021 Last updated: Sep 08, 2021	Comment: This variant is associated with the following publications: (PMID: 30414346)
Benign (Feb 18, 2021)	criteria provided, single submitter (Sema4 Curation Guidelines) Method: curation	Xeroderma pigmentosum Affected status: unknown Allele origin: germline	Sema4, Sema4 Accession: SCV002537002.1 First in ClinVar: Jun 24, 2022 Last updated: Jun 24, 2022
Benign (Jul 13, 2022)	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Women's Health and Genetics/Laboratory Corporation of America, LabCorp Accession: SCV002570821.1 First in ClinVar: Sep 17, 2022 Last updated: Sep 17, 2022	Publications: PubMed (2) PubMed: 30414346‚ 33558524 Comment: Variant summary: POLH c.626G>T (p.Gly209Val) results in a non-conservative amino acid change located in the UmuC domain (IPR001126) of the encoded protein sequence. Five of … (more) Variant summary: POLH c.626G>T (p.Gly209Val) results in a non-conservative amino acid change located in the UmuC domain (IPR001126) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0038 in 251482 control chromosomes, predominantly at a frequency of 0.01 within the South Asian subpopulation in the gnomAD database, including 3 homozygotes. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 34-fold of the estimated maximal expected allele frequency for a pathogenic variant in POLH causing Xeroderma Pigmentosum phenotype (0.0003), strongly suggesting that the variant is a benign polymorphism found primarily in populations of South Asian origin. c.626G>T has been reported in the literature in individuals affected with melanoma and suspected HBOC (Potjer_2019, Moradian_2021). These reports do not provide unequivocal conclusions about association of the variant with Xeroderma Pigmentosum. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five ClinVar submitters (evaluation after 2014) cite the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign. (less)
Benign (Jan 29, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001100564.5 First in ClinVar: Dec 17, 2019 Last updated: Feb 20, 2024
Benign (Apr 01, 2024)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV004161698.10 First in ClinVar: Nov 20, 2023 Last updated: Oct 20, 2024	Comment: POLH: BS1, BS2 Number of individuals with the variant: 17
Benign (-)	no assertion criteria provided Method: clinical testing	Xeroderma pigmentosum variant type Affected status: yes Allele origin: germline	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV000734499.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018
Benign (-)	no assertion criteria provided Method: clinical testing	Breast Cancer Affected status: yes Allele origin: germline	Center of Medical Genetics and Primary Health Care Accession: SCV001449153.1 First in ClinVar: Dec 11, 2020 Last updated: Dec 11, 2020
Benign (Sep 17, 2017)	no assertion criteria provided (ACGS Guidelines, 2013) Method: clinical testing	Xeroderma pigmentosum variant type Affected status: yes Allele origin: germline	Genome Diagnostics Laboratory, Amsterdam University Medical Center Study: VKGL Data-share Consensus Accession: SCV000745891.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018
Benign (-)	no assertion criteria provided Method: clinical testing	not specified Affected status: yes Allele origin: germline	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center Additional submitter: Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001975375.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021
click to load more click to collapse

Comment:

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

Comment:

Variant summary: POLH c.626G>T (p.Gly209Val) results in a non-conservative amino acid change located in the UmuC domain (IPR001126) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0038 in 251482 control chromosomes, predominantly at a frequency of 0.01 within the South Asian subpopulation in the gnomAD database, including 3 homozygotes. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 34-fold of the estimated maximal expected allele frequency for a pathogenic variant in POLH causing Xeroderma Pigmentosum phenotype (0.0003), strongly suggesting that the variant is a benign polymorphism found primarily in populations of South Asian origin. c.626G>T has been reported in the literature in individuals affected with melanoma and suspected HBOC (Potjer_2019, Moradian_2021). These reports do not provide unequivocal conclusions about association of the variant with Xeroderma Pigmentosum. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five ClinVar submitters (evaluation after 2014) cite the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Germline mutational spectrum in Armenian breast cancer patients suspected of hereditary breast and ovarian cancer.	Moradian MM	Human genome variation	2021	PMID: 33558524
Multigene panel sequencing of established and candidate melanoma susceptibility genes in a large cohort of Dutch non-CDKN2A/CDK4 melanoma families.	Potjer TP	International journal of cancer	2019	PMID: 30414346

Text-mined citations for rs2307456 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 20, 2024

ClinVar Genomic variation as it relates to human health

NM_006502.3(POLH):c.626G>T (p.Gly209Val)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs2307456 ...