BMPR2 c.1276+16A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, nfe)
Conditions
1
Primary pulmonary hypertension
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +16 | near-intronic (+16 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP -4.1, phastCons 0.63 |
| Non-coding constraint | Z 4.11 | 1 kb window · o/e 0.61 · regional · uncalibrated |
| Overall | ||
| CADD | 4.469 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
European (non-Finnish) · 131/1,179,324 alleles
Filtering AF
0.00953%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00896%
Overall
0.00833%
134/1,609,202 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0111% | 9,002 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,808 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BMPR2
- Coding
- c.1276+16A>C
- MANE Select
- NM_001204
- dbSNP
- rs753682147
- Type
- single nucleotide variant
- Location
- chr2:202532748 (GRCh38)
- Gene constraint
- LOEUF 0.376 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.07 · 7 PDB
Similar variants
- BMPR2 c.1128+1G>A Pathogenic ★★ same condition
- BMPR2 c.1128+1G>C Pathogenic ★★ same condition
- BMPR2 c.621+1G>T Pathogenic/Likely pathogenic ★★ same condition
- BMPR2 c.853-2A>G Pathogenic ★★ same condition
- BMPR2 p.Arg147Ter Pathogenic ★★ same condition
- BMPR2 p.Arg213Ter Pathogenic ★★ same condition
- BMPR2 p.Arg491Trp Pathogenic ★★ same condition
- BMPR2 p.Arg873Ter Pathogenic/Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bmpr2-c-1276-plus-16a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown