FAP p.Ala100=
c.300T>C · rs78244369 · VCV774834
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.757%, nfe)
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 5.2 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 10.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.757%
European (non-Finnish) · 8,866/1,171,776 alleles
Filtering AF
0.743%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.738%
Overall
0.608%
9,696/1,595,246 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.757% | 132 |
| Remaining individualsnot grpmax-eligible | 0.484% | 207 |
| Finnishnot grpmax-eligible | 0.285% | 350 |
| Admixed American | 0.19% | 525 |
| South Asian | 0.169% | 593 |
| Middle Eastern | 0.118% | 844 |
| African / African-American | 0.106% | 940 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0307% | 3,253 |
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
- FAP
- Protein
- p.Ala100=
- Coding
- c.300T>C
- MANE Select
- NM_004460
- dbSNP
- rs78244369
- Type
- single nucleotide variant
- Location
- chr2:162224526 (GRCh38)
- Gene constraint
- LOEUF 0.892 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.72 · 4 PDB
Similar variants
- FAP c.1870-8C>A Benign ★★ same type
- FAP p.Gln708= Benign ★★ same type
- FAP p.Gly195= Benign ★★ same type
- FAP p.Leu212Phe Benign ★★ same type
- FAP p.Phe185Leu Likely benign ★★ same type
- FAP p.Ser737= Likely benign ★★ same type
- FAP p.Thr229Met Benign ★★ ⚠ same type
- FAP p.Tyr458= Benign ★★ 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/fap-p-ala100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown