CDKN1B p.Ala103=
c.309G>C · rs761029896 · VCV1727578
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Conditions
2
hereditary neoplastic syndrome
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 0.66 | GERP -1.6, phastCons 0.98 |
| Overall | ||
| CADD | 6.781 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,086 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,614,026 alleles · very rare
exomes 3/1,461,668 · genomes 0/152,358 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,086 |
| European (non-Finnish) | 0.000169% | 589,998 |
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
- CDKN1B
- Protein
- p.Ala103=
- Coding
- c.309G>C
- MANE Select
- NM_004064
- dbSNP
- rs761029896
- Type
- single nucleotide variant
- Location
- chr12:12718148 (GRCh38)
- Gene constraint
- LOEUF 0.804 · pLI 0.24 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.08 · 19 PDB
- Residue 103
- the 'disordered' region
Similar variants
- CDKN1B p.Ala103Thr Uncertain significance ★★ ⚠ same residue
- CDKN1B p.Ala103Val Conflicting classifications of pathogenicity ★ ⚠ same residue
- CDKN1B p.Arg154Ter Pathogenic ★★ same condition
- CDKN1B p.Arg5Ter Pathogenic/Likely pathogenic ★★ same condition
- CDKN1B p.Gln104Ter Pathogenic ★★ same condition
- CDKN1B p.Gln107Ter Pathogenic ★★ same condition
- CDKN1B p.Gln141Ter Pathogenic ★★ same condition
- CDKN1B p.Gln163Ter 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/cdkn1b-p-ala103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown