LRFN5 p.Phe147=
c.441C>T · rs117966123 · VCV3042008
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.66%, sas)
Conditions
1
LRFN5-related disorder
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 0.26 | GERP -1.5, phastCons 0.99 |
| Overall | ||
| CADD | 10.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.66%
South Asian · 1,513/91,086 alleles
Filtering AF
1.59%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.56%
Overall
1.12%
18,052/1,614,038 alleles · low-frequency
exomes 16,821/1,461,742 · genomes 1,231/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.66% | 60 |
| Middle Eastern | 1.63% | 61 |
| Ashkenazi Jewishnot grpmax-eligible | 1.58% | 63 |
| European (non-Finnish) | 1.24% | 81 |
| Remaining individualsnot grpmax-eligible | 1.04% | 96 |
| Finnishnot grpmax-eligible | 0.557% | 179 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| Admixed American | 0.32% | 313 |
| African / African-American | 0.211% | 475 |
| East Asian | 0.00446% | 22,440 |
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
- LRFN5
- Protein
- p.Phe147=
- Coding
- c.441C>T
- MANE Select
- NM_152447
- dbSNP
- rs117966123
- Type
- single nucleotide variant
- Location
- chr14:41887066 (GRCh38)
- Gene constraint
- LOEUF 0.629 · pLI 0.17 (gnomAD)
- Structure
- AlphaFold pLDDT 74.66 · 4 PDB
Disease context
LRFN5-related disorder
Similar variants
- LRFN5 p.Ala59= Benign same condition
- LRFN5 p.Arg681= Likely benign same condition
- LRFN5 p.Glu315= Likely benign same condition
- LRFN5 p.Glu717= Benign same condition
- LRFN5 p.Phe544Val Likely benign ⚠ same condition
- LRFN5 p.Ser522= Benign same condition
- LRFN5 p.Ser622Phe Benign same condition
- LRFN5 p.Ser685= Benign 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/lrfn5-p-phe147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown