LFNG p.Ala170=
c.510C>T · VCV4895024
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 -20 | GERP -3.1 |
| Overall | ||
| CADD | 0.371 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,008 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00083%
Overall
0.00149%
24/1,612,814 alleles · very rare
exomes 22/1,460,548 · genomes 2/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,003 |
| European (non-Finnish) | 0.00161% | 62,101 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,456 |
| South Asian | 0.0011% | 91,090 |
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
- LFNG
- Protein
- p.Ala170=
- Coding
- c.510C>T
- MANE Select
- NM_001040167
- Type
- single nucleotide variant
- Location
- chr7:2525247 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI 0.02 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.66
Similar variants
- LFNG p.Ala170Thr Uncertain significance ★ ⚠ same residue
- LFNG p.Thr145Met Likely pathogenic ★★ same type
- LFNG c.482-3C>T Uncertain significance ★★ same type
- LFNG p.Ala95Val Uncertain significance ★★ ⚠ same type
- LFNG p.Ala99Thr Uncertain significance ★★ ⚠ same type
- LFNG p.Arg187Cys Uncertain significance ★★ ⚠ same type
- LFNG p.Arg239Trp Uncertain significance ★★ ⚠ same type
- LFNG p.Arg246His 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/lfng-p-ala170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown