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NM_001204.7(BMPR2):c.-93A>G AND Pulmonary arterial hypertension

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Apr 30, 2024
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV003150164.2

Allele description [Variation Report for NM_001204.7(BMPR2):c.-93A>G]

NM_001204.7(BMPR2):c.-93A>G

Gene:
BMPR2:bone morphogenetic protein receptor type 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q33.1
Genomic location:
Preferred name:
NM_001204.7(BMPR2):c.-93A>G
HGVS:
  • NC_000002.12:g.202377382A>G
  • NG_009363.1:g.6056A>G
  • NM_001204.7:c.-93A>GMANE SELECT
  • LRG_712t1:c.-93A>G
  • LRG_712:g.6056A>G
  • NC_000002.11:g.203242105A>G
  • NM_001204.6:c.-93A>G
Links:
dbSNP: rs147936167
NCBI 1000 Genomes Browser:
rs147936167
Molecular consequence:
  • NM_001204.7:c.-93A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
Observations:
1

Condition(s)

Name:
Pulmonary arterial hypertension
Identifiers:
MONDO: MONDO:0015924; MeSH: D000081029; MedGen: C2973725; Orphanet: 182090; Human Phenotype Ontology: HP:0002092

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003837589Institute of Human Genetics, University of Wuerzburg
no assertion criteria provided
Uncertain significanceunknownclinical testing

SCV005043322Clingen Pulmonary Hypertension Variant Curation Expert Panel, ClinGen
reviewed by expert panel

(ClinGen PH ACMG Specifications BMPR2 V1.1.0)		Likely Benign
(Apr 30, 2024) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration
not providedunknownyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Institute of Human Genetics, University of Wuerzburg, SCV003837589.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

From Clingen Pulmonary Hypertension Variant Curation Expert Panel, ClinGen, SCV005043322.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The BMPR2 NM_001204.7(BMPR2):c.-93A>G variant is a 5' UTR variant. The highest population minor allele frequency in gnomAD v2.1.1 controls is 0.006608 (6/908 alleles) in the East Asian population, which is higher than the ClinGen Pulmonary Hypertension VCEP threshold of >0.1% for BS1, and therefore meets this criterion (BS1). No functional data was available for review and multiple lines of computational evidence suggest no impact on the gene (BP4). No other criteria were met. In summary, the variant meets the criteria to be classified as likely benign for pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: BS1, BP4 [VCEP specification version 1.1, 1/18/2024].

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

Last Updated: Sep 29, 2024