F13A1 p.Phe540=
c.1620C>T · rs142891701 · VCV716120
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.58%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 6.065 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.58%
African / African-American · 435/75,022 alleles
Filtering AF
0.535%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.517%
Overall
0.0284%
459/1,614,158 alleles · rare
exomes 225/1,461,886 · genomes 234/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.58% | 172 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.0133% | 7,503 |
| European (non-Finnish) | 0.000254% | 393,346 |
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
- F13A1
- Protein
- p.Phe540=
- Coding
- c.1620C>T
- MANE Select
- NM_000129
- dbSNP
- rs142891701
- Type
- single nucleotide variant
- Location
- chr6:6174707 (GRCh38)
- Gene constraint
- LOEUF 0.734 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.15 · 15 PDB
- Residue 540
- a β-strand
Similar variants
- F13A1 c.691-1G>A Pathogenic/Likely pathogenic ★★ same type
- F13A1 p.Arg327Gln Pathogenic/Likely pathogenic ★★ same type
- F13A1 p.Arg409Gln Likely pathogenic ★★ ⚠ same type
- F13A1 p.Arg662Ter Pathogenic ★★ same type
- F13A1 p.Arg682His Pathogenic ★★ ⚠ same type
- F13A1 p.Arg78Cys Pathogenic/Likely pathogenic ★★ same type
- F13A1 p.Gly274Arg Likely pathogenic ★★ same type
- F13A1 c.*1045C>G 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/f13a1-p-phe540 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown