U.S. flag

An official website of the United States government

NM_012203.2(GRHPR):c.734+9G>A AND Primary hyperoxaluria, type II

Germline classification:
Benign/Likely benign (4 submissions)
Last evaluated:
Jul 21, 2021
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:
RCV000186432.9

Allele description [Variation Report for NM_012203.2(GRHPR):c.734+9G>A]

NM_012203.2(GRHPR):c.734+9G>A

Gene:
GRHPR:glyoxylate and hydroxypyruvate reductase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p13.2
Genomic location:
Preferred name:
NM_012203.2(GRHPR):c.734+9G>A
HGVS:
  • NC_000009.12:g.37430655G>A
  • NG_008135.1:g.12946G>A
  • NM_012203.2:c.734+9G>AMANE SELECT
  • NC_000009.11:g.37430652G>A
  • NM_012203.1:c.734+9G>A
Links:
dbSNP: rs56401536
NCBI 1000 Genomes Browser:
rs56401536
Molecular consequence:
  • NM_012203.2:c.734+9G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Primary hyperoxaluria, type II (HP2)
Synonyms:
OXALOSIS II; Primary hyperoxaluria type 2; Oxalosis 2; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009824; MedGen: C0268165; Orphanet: 416; Orphanet: 93599; OMIM: 260000

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000239784Clinical Biochemistry Laboratory, Health Services Laboratory
no assertion criteria provided
Uncertain significance
(Nov 27, 2014)
germlineresearch

Citation Link,

SCV000480140Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Benign
(Jan 13, 2018)
germlineclinical testing

Citation Link,

SCV002075687Natera, Inc.
no assertion criteria provided
Benign
(Dec 2, 2019)
germlineclinical testing

SCV002811219Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(Jul 21, 2021)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedresearch

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 Clinical Biochemistry Laboratory, Health Services Laboratory, SCV000239784.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV000480140.3

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

Description

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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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

From Natera, Inc., SCV002075687.1

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

From Fulgent Genetics, Fulgent Genetics, SCV002811219.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024