Evidence Repository
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
  • No CSPEC computer assertion could be determined for this classification!

Variant: NM_001204.7(BMPR2):c.419-38del

CA2061113

548685 (ClinVar)

Gene: BMPR2
Condition: pulmonary arterial hypertension
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 0c966759-6fc4-4b90-a60b-dbe8e70736b5
Approved on: 2024-05-03
Published on: 2024-05-03

HGVS expressions

NM_001204.7:c.419-38del
NM_001204.7(BMPR2):c.419-38del
NC_000002.12:g.202513681del
CM000664.2:g.202513681del
NC_000002.11:g.203378404del
CM000664.1:g.203378404del
NC_000002.10:g.203086649del
NG_009363.1:g.142355del
ENST00000374580.10:c.419-38del
ENST00000638587.1:c.350-38del
ENST00000374574.2:c.419-38del
ENST00000374580.8:c.419-38del
NM_001204.6:c.419-38del
More

Benign

Met criteria codes 3
BS2 BP4 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 c.419-38del is an intronic variant at Intron 3. The highest population minor allele frequency in gnomAD v2.1.1 (controls) is 0.1814 (2514/13856 alleles) in European (Finnish) population, which is higher than the ClinGen Pulmonary Hypertension Expert Panel threshold (>0.01) for BA1, and therefore meets this stand-alone criterion (BA1). This variant has been observed in 1160 times in homozygous state in healthy individuals (BS2). The computational splicing predictor SpliceAI gives a score of (0.00) for acceptor splice site loss suggesting that the variant has no impact on splicing (BP4). In summary, the variant is classified as benign for pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: BA1, BS2, BP4 (VCEP specification version v 1.1, 1/18/2024).
Met criteria codes
BS2
This variant has been observed in 1160 times in homozygous state in healthy individuals.
BP4
The computational splicing predictor SpliceAI gives a score of (0.00) for acceptor loss suggesting that the variant has no impact on splicing.
BA1
The highest population minor allele frequency in gnomAD v2.1.1 controls is 0.1814 (2514/13856 alleles) in European (Finnish) population, which is higher than the ClinGen Pulmonary Hypertension VCEP threshold of (>0.01) for BA1, and therefore meets this stand-alone criterion.
Curation History
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