The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_001204.7(BMPR2):c.1512T>G (p.Leu504=)

CA2061382

898481 (ClinVar)

Gene: BMPR2 (HGNC:659)
Condition: pulmonary arterial hypertension (MONDO:0015924)
Inheritance Mode: Autosomal dominant inheritance
UUID: 31b37b7a-c652-4665-b6e0-a563c20d152d
Approved on: 2024-05-02
Published on: 2024-05-02

HGVS expressions

NM_001204.7(BMPR2):c.1512T>G (p.Leu504=)
NM_001204.7:c.1512T>G
NC_000002.12:g.202552814T>G
CM000664.2:g.202552814T>G
NC_000002.11:g.203417537T>G
CM000664.1:g.203417537T>G
NC_000002.10:g.203125782T>G
NG_009363.1:g.181488T>G
ENST00000374580.10:c.1512T>G
ENST00000638587.1:c.1443T>G
ENST00000374574.2:c.1512T>G
ENST00000374580.8:c.1512T>G
NM_001204.6:c.1512T>G
More

Likely Benign

Met criteria codes 2
BP7 BP4
Not Met criteria codes 3
BA1 BS1 PM2

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.1512T>G;p.(leu504=) variant is a synonymous (silent) variant that is not predicted by SpliceAI to impact splicing. The highest population minor allele frequency in gnomAD v2.1.1 controls is 0.0138% (2/14452 alleles) in the North-Western European population, which is lower than the ClinGen Pulmonary Hypertension VCEP threshold of >0.1% for BS1 and >1% for BA1, but higher than the threshold of <0.01% for PM2 (BS1, BA1 and PM2 are not met). BS2 was not met as the variant was not observed as a homozygous allele in gnomAD v2.1.1 controls. BP4 is met based on the computational predictor, CADD, giving a score of 8.3 which is below the threshold of ≤10.0 for BP4. Due to the absence of segregation data, PP1, PM6 and PS2 could not be evaluated. Due to absence of functional data, BS3 and PS3 could not be evaluated. In summary, the variant meets the criteria to be classified as a likely benign variant for pulmonary arterial hypertension based on the ACMG/AMP criteria applied, as specified by the ClinGen Pulmonary Hypertension VCEP: BP4, BP7 (VCEP specification version 1.1, 1/18/2024).
Met criteria codes
BP7
SpliceAI: 0.00 (no loss or gain of splice sites) Vertebrate PhyloP: -0.023 (nucleotide not conserved)
BP4
CADD score is <10 with 8.3 (GRCh37-v.1.7); REVEL not applicable
Not Met criteria codes
BA1
GnomAD v.2.1.1 controls: 0.014% (2/14452 alleles) in North West Europeans with >1000 allele counts, which is not greater than 1%
BS1
GnomAD v.2.1.1 controls: 0.014% (2/14452 alleles) in North West Europeans with >1000 allele counts, which is smaller than 0.1%
PM2
GnomAD v.2.1.1 controls: 0.014% (2/14452 alleles) in North West Europeans with >1000 allele counts, which is higher than the cut-off value for PM2 of 0.01%
Curation History
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