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.2656C>T (p.Arg886Cys)

CA2061559

458626 (ClinVar)

Gene: BMPR2
Condition: pulmonary arterial hypertension
Inheritance Mode: Autosomal dominant inheritance
UUID: f559bee5-7640-4263-99c6-7feea7742bdb
Approved on: 2024-09-10
Published on: 2024-09-10

HGVS expressions

NM_001204.7:c.2656C>T
NM_001204.7(BMPR2):c.2656C>T (p.Arg886Cys)
NC_000002.12:g.202556321C>T
CM000664.2:g.202556321C>T
NC_000002.11:g.203421044C>T
CM000664.1:g.203421044C>T
NC_000002.10:g.203129289C>T
NG_009363.1:g.184995C>T
ENST00000374580.10:c.2656C>T
ENST00000638587.1:c.2587C>T
ENST00000374574.2:c.1587-3375C>T
ENST00000374580.8:c.2656C>T
NM_001204.6:c.2656C>T
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Likely Benign

Met criteria codes 1
BS1
Not Met criteria codes 7
PS4 BA1 PP3 PM2 PM1 BS2 BP4

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.2656C>T variant is a missense variant predicted to cause an arginine to cysteine substitution at amino acid position 886. The highest population minor allele frequency in gnomAD v.2.1.1 controls is 0.1130% (11/9738 alleles) in the African/African American population. The population evidence available meets the threshold for BS1 (≥0.1%), but not for BA1 (>5%) or PM2 (<0.01%) as defined by the ClinGen Pulmonary Hypertension VCEP (PH-VCEP). Computational evidence for pathogenicity as evaluated by REVEL generated a score of 0.485 indicating that neither BP4 or PP3 were met since the threshold specified by the PH-VCEP is <0.25 and >0.75, respectively. The amino acid substitution occurs in the c-terminal domain, which is not a well-established functional domain, so PM1 was not met. Criteria not evaluated included PP1, PM6, and PS2 due to the absence of segregation data. BS3 and PS3 were not evaluated due to the lack of functional data for this variant. In summary, the variant meets the criteria to be classified as likely benign (LB) for pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: BS1 (VCEP specification version 1.1, 1/18/2024).
Met criteria codes
BS1
AF of variant on gnomAD v2.1.1 is 0.1130%, which meets the threshold of >=0.1% defined by the pulmonary hypertension expert panel.
Not Met criteria codes
PS4
There is one submission on ClinVar but PM2 is not met. Based on the BMPR2-specific guidelines developed by the pulmonary hypertension expert panel, PM2 must be met to apply the PS4 criterion.
BA1
AF of variant on gnomAD v2.1.1 is 0.1130%, which is lower than the threshold of >5% defined by the pulmonary hypertension expert panel.
PP3
REVEL score is 0.485, which is lower than the >0.75 cut-off defined by the pulmonary hypertension expert panel.
PM2
AF of variant on gnomAD v2.1.1 is 0.1130%, which is a higher than the threshold of <0.01% defined by the pulmonary hypertension expert panel.
PM1
Variant is predicted to cause a substitution of an Arginine residue for a Cysteine in position 886 in the BMPR2 protein. This change occurs in the C-terminal domain, which is not a well established functional domain.
BS2
No homozygotes observed on gnomAD v2.1.1
BP4
REVEL score is 0.485, which is higher than the <0.25 cut-off defined by the pulmonary hypertension expert panel.
Curation History
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