LFNG p.Ala9=
c.27G>T · rs143245520 · VCV2657231
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.236%, 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 -5.1 | GERP -1.5 |
| Overall | ||
| CADD | 2.544 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.236%
European (non-Finnish) · 2,752/1,165,954 alleles
Filtering AF
0.229%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.226%
Overall
0.198%
3,172/1,598,366 alleles · rare
exomes 2,932/1,446,040 · genomes 240/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.236% | 424 |
| Admixed American | 0.207% | 484 |
| Remaining individualsnot grpmax-eligible | 0.174% | 574 |
| South Asian | 0.171% | 586 |
| Middle Eastern | 0.0497% | 2,012 |
| African / African-American | 0.0228% | 4,395 |
| Finnishnot grpmax-eligible | 0.0188% | 5,313 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00339% | 29,494 |
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.Ala9=
- Coding
- c.27G>T
- MANE Select
- NM_001040167 · reported on NM_002304
- dbSNP
- rs143245520
- Type
- single nucleotide variant
- Location
- chr7:2518580 (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.Leu9= Likely benign ★ 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-ala9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown