VCV000348165.10 - ClinVar

NM_000320.3(QDPR):c.-81del

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.

(3)

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_000320.3(QDPR):c.-81del

Variation ID: 348165 Accession: VCV000348165.10

Type and length

Deletion, 1 bp

Location

Cytogenetic: 4p15.32 4: 17512135 (GRCh38) [ NCBI UCSC ] 4: 17513758 (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	Dec 6, 2016	Dec 31, 2022	Jul 19, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NM_000320.3:c.-81del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NM_000320.2:c.-81delC
NM_001306140.1:c.-81delC
NR_156494.1:n.100delC
NC_000004.12:g.17512135del
NC_000004.11:g.17513758del
NG_008763.1:g.5100del
NG_171750.1:g.517del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000004.12:17512134:G:

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.

0.18191 ()

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

1000 Genomes Project 0.18191

1000 Genomes Project 30x 0.18254

Trans-Omics for Precision Medicine (TOPMed) 0.21319

The Genome Aggregation Database (gnomAD) 0.22322

Links

ClinGen: CA10617457 dbSNP: rs67496406 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.
LOC129992304	-	-	-	GRCh38	-	86
QDPR		-	-	GRCh38 GRCh37	304	425

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.
BH4-Deficient Hyperphenylalaninemia	Likely benign (1)	criteria provided, single submitter	Jun 14, 2016	RCV000272562.14
not provided	Benign (1)	criteria provided, single submitter	Nov 20, 2018	RCV001672640.11
Dihydropteridine reductase deficiency	Benign (1)	criteria provided, single submitter	Jul 19, 2021	RCV002502340.8

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.
Likely benign (Jun 14, 2016)	criteria provided, single submitter (ICSL Variant Classification 20161018) Method: clinical testing	BH4-Deficient Hyperphenylalaninemia Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000448619.2 First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016
Benign (Nov 20, 2018)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001889471.1 First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021
Benign (Jul 19, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Dihydropteridine reductase deficiency Affected status: unknown Allele origin: unknown	Fulgent Genetics, Fulgent Genetics Accession: SCV002808402.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022

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.

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs67496406 ...

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 Nov 25, 2024

ClinVar Genomic variation as it relates to human health

NM_000320.3(QDPR):c.-81del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs67496406 ...