LIN28A p.Ala29=
c.87C>G · rs116719577 · VCV711821
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.86%, afr)
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 -0.16 | GERP -0.29, phastCons 0.046 |
| Overall | ||
| CADD | 8.974 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.86%
African / African-American · 3,644/74,904 alleles
Filtering AF
4.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.68%
Overall
0.252%
4,055/1,608,954 alleles · low-frequency
exomes 1,981/1,456,632 · genomes 2,074/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.86% | 21 |
| Admixed American | 0.315% | 317 |
| Remaining individualsnot grpmax-eligible | 0.272% | 368 |
| Middle Eastern | 0.122% | 821 |
| European (non-Finnish) | 0.00382% | 26,175 |
| South Asian | 0.00331% | 30,243 |
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
- LIN28A
- Protein
- p.Ala29=
- Coding
- c.87C>G
- MANE Select
- NM_024674
- dbSNP
- rs116719577
- Type
- single nucleotide variant
- Location
- chr1:26411441 (GRCh38)
- Gene constraint
- LOEUF 0.831 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 76.53 · 8 PDB
- Residue 29
- the 'disordered' region
Similar variants
- LIN28A p.Leu176Val Uncertain significance ★★ ⚠ same type
- LIN28A p.Ala16Thr Uncertain significance ★ ⚠ same type
- LIN28A p.Ala32Thr Uncertain significance ★ ⚠ same type
- LIN28A p.Ala32Val Uncertain significance ★ ⚠ same type
- LIN28A p.Ala92Ser Uncertain significance ★ ⚠ same type
- LIN28A p.Arg123Gln Uncertain significance ★ ⚠ same type
- LIN28A p.Arg192Gln Uncertain significance ★ ⚠ same type
- LIN28A p.Arg61Ser Uncertain significance ★ ⚠ same type
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/lin28a-p-ala29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown