Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA10613575

333636 (ClinVar)

Gene: BMPR2

Condition: pulmonary arterial hypertension

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 068fe37c-6ccb-4f7d-8daf-425aa1384a70

Approved on: 2024-04-30

Published on: 2024-04-30

HGVS expressions

NM_001204.7:c.-93A>G

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

NC_000002.12:g.202377382A>G

CM000664.2:g.202377382A>G

NC_000002.11:g.203242105A>G

CM000664.1:g.203242105A>G

NC_000002.10:g.202950350A>G

NG_009363.1:g.6056A>G

ENST00000374580.10:c.-93A>G

ENST00000374580.8:c.-93A>G

NM_001204.6:c.-93A>G

Likely Benign

BS1 BP4

PM2 BA1 PP3

Evidence Links 0

Expert Panel

Pulmonary Hypertension VCEP

Criteria Specification Information

Criteria Specification: ClinGen Pulmonary Hypertension Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BMPR2 Version 1.1.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Pulmonary Hypertension VCEP

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].

BS1

The variant is found in the East Asian population on gnomAD v2.1.1 (controls) with a frequency of 0.006608 (6/908), which is greater than the PH-VCEP cut-off for PM2 (<0.0001) and lower than the cut-off for BS1 (>0.1%) and BA1 (>1%).

BP4

The CADD score for this variant is 9.060 (Chr 2, Position 203242105, CADD GRCh37-v1.7), which is lower than the PH-VCEP cut-off of <10. SpliceAI is 0, no splicing effect predicted.

PM2

BS1 is met

BA1

BS1 is met

PP3

BP4 is met

Curation History

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