The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_001204.7(BMPR2):c.-93A>G

CA10613575

333636 (ClinVar)

Gene: BMPR2
Condition: pulmonary arterial hypertension
Inheritance Mode: Autosomal dominant inheritance
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
More

Likely Benign

Met criteria codes 2
BS1 BP4
Not Met criteria codes 3
PP3 PM2 BA1

Evidence Links 0

Expert Panel

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].
Met criteria codes
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.
Not Met criteria codes
PP3
BP4 is met
PM2
BS1 is met
BA1
BS1 is met
Curation History
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