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.2526G>T (p.Arg842Ser)

CA2061546

1398400 (ClinVar)

Gene: BMPR2
Condition: pulmonary arterial hypertension
Inheritance Mode: Autosomal dominant inheritance
UUID: d12c3caa-4bb0-4292-acb4-ae0e8ae64e24
Approved on: 2024-09-10
Published on: 2024-09-10

HGVS expressions

NM_001204.7:c.2526G>T
NM_001204.7(BMPR2):c.2526G>T (p.Arg842Ser)
NC_000002.12:g.202556191G>T
CM000664.2:g.202556191G>T
NC_000002.11:g.203420914G>T
CM000664.1:g.203420914G>T
NC_000002.10:g.203129159G>T
NG_009363.1:g.184865G>T
ENST00000374580.10:c.2526G>T
ENST00000638587.1:c.2457G>T
ENST00000374574.2:c.1586+3303G>T
ENST00000374580.8:c.2526G>T
NM_001204.6:c.2526G>T

Uncertain Significance

Met criteria codes 1
PM2_Supporting
Not Met criteria codes 6
BS1 BP4 PS1 PP3 PM1 PM5

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.1882A>G variant is a missense variant predicted to result in an arginine to serine substitution at amino acid position 842 (p.Arg842Ser). The highest population minor allele frequency in gnomAD v.2.1.1 controls is 0.000070 in the European (non-Finnish) population thus meeting the threshold for PM2_supporting, resultantly neither BS1 nor BA1 were met. Computational evidence for pathogenicity as evaluated by REVEL generated a score of 0.468 indicating that neither BP4 nor PP3 were met. Additionally, the SpliceAI algorithm predicts no deleterious impact on putative acceptor or donor splice sites. The BMPR2 C-terminus is of unclear functional and/or structural relevance, hence PM1 is not met. Due to no evidence of familial segregation PP1, PM6 and PS2 were not assessed. BS3 and PS3 were not evaluated as functional data is unavailable for this variant. In summary, the variant meets the criteria to be classified as a variant of uncertain significance (VUS) for pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: PM2_supporting (VCEP specification version 1.1, 1/18/2024).
Met criteria codes
PM2_Supporting
Allele frequency in European (non-Finnish) population (gnomAD v2.1.1 controls) is less than 0.01% (MAF: 3/42744 = 0.000070)
Not Met criteria codes
BS1
Allele frequency is less than 0.01% in gnomAD v2.1.1 controls.
BP4
REVEL score is 0.468 hence does not meet the threshold to be classified as benign (REVEL<0.25)
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL score is 0.468 hence does not meet the threshold to be classified as deleterious (REVEL>0.75)
PM1
Variant is located in the C-terminus, of unclear functional and/or structural relevance.
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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