MFAP5 p.Phe11=
c.33T>C · rs769973987 · VCV2987177
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.125 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.93 | GERP -3.7 |
| Overall | ||
| CADD | 3.169 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,014 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,613,924 alleles · very rare
exomes 3/1,461,626 · genomes 0/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,014 |
| European (non-Finnish) | 0.000169% | 590,012 |
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
- MFAP5
- Protein
- p.Phe11=
- Coding
- c.33T>C
- MANE Select
- NM_003480
- dbSNP
- rs769973987
- Type
- single nucleotide variant
- Location
- chr12:8662072 (GRCh38)
- Gene constraint
- LOEUF 0.975 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.79
Similar variants
- MFAP5 p.Phe11Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- MFAP5 c.140-3C>A Uncertain significance ★★ same type
- MFAP5 c.217+1G>T Uncertain significance ★★ same type
- MFAP5 c.247+1G>C Uncertain significance ★★ same type
- MFAP5 c.335+4A>G Uncertain significance ★★ same type
- MFAP5 c.336-3C>T Uncertain significance ★★ same type
- MFAP5 p.Arg115His Uncertain significance ★★ same type
- MFAP5 p.Arg126Cys 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/mfap5-p-phe11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown