F5 p.Asp721=
c.2163T>C · rs1317417517 · VCV1786955
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Conditions
1
Inborn genetic diseases
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 -0.6 | GERP -3.8 |
| Overall | ||
| CADD | 0.669 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,179,996 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,461,828 alleles · very rare
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
- F5
- Protein
- p.Asp721=
- Coding
- c.2163T>C
- MANE Select
- NM_000130
- dbSNP
- rs1317417517
- Type
- single nucleotide variant
- Location
- chr1:169542927 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.57 · 23 PDB
- Residue 721
- a β-strand; the 'b' region
Similar variants
- F5 p.Arg441His Uncertain significance ★★ ⚠ same condition
- F5 p.Asn1559Ser Uncertain significance ★★ ⚠ same condition
- F5 p.Asn1575Ser Uncertain significance ★★ ⚠ same condition
- F5 p.Asp1739Gly Uncertain significance ★★ ⚠ same condition
- F5 p.Glu2029Asp Uncertain significance ★★ ⚠ same condition
- F5 p.Glu48Gln Uncertain significance ★★ ⚠ same condition
- F5 p.His812Tyr Uncertain significance ★★ ⚠ same condition
- F5 p.Ile1558Val Uncertain significance ★★ ⚠ 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/f5-p-asp721 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown