ABCC9 p.Val32=
c.96C>T · rs727505034 · VCV179664
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0659%, sas)
Conditions
2
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.31 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.33 | GERP -0.027, phastCons 0.92 |
| Overall | ||
| CADD | 5.333 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0659%
South Asian · 60/91,026 alleles
Filtering AF
0.0526%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0477%
Overall
0.00506%
74/1,461,048 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0659% | 1,517 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,823 |
| African / African-American | 0.00133% | 74,944 |
| European (non-Finnish) | 0.000848% | 117,935 |
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
- ABCC9
- Protein
- p.Val32=
- Coding
- c.96C>T
- MANE Select
- NM_020297
- dbSNP
- rs727505034
- Type
- single nucleotide variant
- Location
- chr12:21936579 (GRCh38)
- Gene constraint
- LOEUF 0.557 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.72
Similar variants
- ABCC9 c.2506-1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCC9 p.Arg1116Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ABCC9 p.Arg1116His Pathogenic ★★ ⚠ same condition
- ABCC9 p.Arg1154Gln Pathogenic ★★ same condition
- ABCC9 p.Arg1154Trp Pathogenic/Likely pathogenic ★★ same condition
- ABCC9 p.Gln852Ter Pathogenic/Likely pathogenic ★★ same condition
- ABCC9 p.Thr1202Met Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ABCC9 p.Val1266Met 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/abcc9-p-val32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown