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.968-5A>G

CA16610662

409829 (ClinVar)

Gene: BMPR2
Condition: pulmonary arterial hypertension
Inheritance Mode: Autosomal dominant inheritance
UUID: cc7890de-9825-43e3-9d6e-06fe2b6a8c9d
Approved on: 2024-05-03
Published on: 2024-05-03

HGVS expressions

NM_001204.7:c.968-5A>G
NM_001204.7(BMPR2):c.968-5A>G
NC_000002.12:g.202530789A>G
CM000664.2:g.202530789A>G
NC_000002.11:g.203395512A>G
CM000664.1:g.203395512A>G
NC_000002.10:g.203103757A>G
NG_009363.1:g.159463A>G
ENST00000374580.10:c.968-5A>G
ENST00000638587.1:c.899-5A>G
ENST00000374574.2:c.968-5A>G
ENST00000374580.8:c.968-5A>G
NM_001204.6:c.968-5A>G
More

Pathogenic

Met criteria codes 4
PS4_Supporting PP3 PM2_Supporting PVS1
Not Met criteria codes 2
BS1 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 NM_001204.7(BMPR2) c.968-5A>G is an intronic variant at Intron 7. This variant is absent from gnomAD v2.1.1 and v3.1.2 controls (PM2_supporting). It is predicted to create a strong acceptor site gain (PP3_supporting) and PH VCEP internal unpublished RNA sequencing data confirmed an effect on splicing leading to NMD. The c.968-5G>A variant leads to the inclusion of 4 bases of intron 7 into the mature mRNA creating a frameshift and a STOP codon at position 327(PVS1_strong). The variant has been reported in 2 unrelated PAH patients: first proband is associated with the publication (PMID: 19555857) and the second proband, with no further information for co-segregation, is from an internal lab contributor (PS4_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: PVS1_strong, PM2_supporting, PS4_supporting and PP3_supporting (VCEP specifications version 1.1, 1/18/2024)
Met criteria codes
PS4_Supporting
The variant has been reported in 3 unrelated PAH patients (1 proband from PMID: 19555857, a ClinVar entry by a clinical laboratory, and 1 from a PH VCEP internal contributor).
PP3
This variant alters the canonical splice donor site of intron 7. Splice AI predicts a strong acceptor gain (score: 0.99).
PM2_Supporting
This variant is absent from gnomAD controls (v2.1.1 and v3.1.2)
PVS1
PH VCEP internal unpublished RNA sequencing data confirmed an effect on splicing leading to NMD. The c.968-5G>A variant leads to the inclusion of 4 bases of intron 7 into the mature mRNA creating a frameshift and a STOP codon at position 327
Not Met criteria codes
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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