ABCC9 p.Leu102=
c.306C>T · rs994917919 · VCV746750
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Conditions
2
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.002 | GERP -3.6, phastCons 0.38 |
| Overall | ||
| CADD | 3.574 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,996 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000372%
6/1,613,972 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,996 |
| European (non-Finnish) | 0.000424% | 236,001 |
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.Leu102=
- Coding
- c.306C>T
- MANE Select
- NM_020297
- dbSNP
- rs994917919
- Type
- single nucleotide variant
- Location
- chr12:21926042 (GRCh38)
- Gene constraint
- LOEUF 0.557 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.72
Similar variants
- ABCC9 p.Leu102Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-leu102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown