FYN p.Phe42=
c.126C>T · rs28763978 · VCV709055
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.82%, afr)
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 2.1 | GERP -0.34, phastCons 1 |
| Overall | ||
| CADD | 11.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.82%
African / African-American · 2,868/75,014 alleles
Filtering AF
3.71%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.66%
Overall
0.201%
3,245/1,614,160 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.82% | 26 |
| Admixed American | 0.267% | 375 |
| Remaining individualsnot grpmax-eligible | 0.243% | 411 |
| Middle Eastern | 0.132% | 758 |
| European (non-Finnish) | 0.00441% | 22,693 |
| South Asian | 0.00439% | 22,770 |
| East Asian | 0.00223% | 44,890 |
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
- FYN
- Protein
- p.Phe42=
- Coding
- c.126C>T
- MANE Select
- NM_002037
- dbSNP
- rs28763978
- Type
- single nucleotide variant
- Location
- chr6:111719926 (GRCh38)
- Gene constraint
- LOEUF 0.215 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.62 · 53 PDB
Similar variants
- FYN p.Asp506Glu Benign ★★ same type
- FYN c.344+1G>A Uncertain significance ★ same type
- FYN p.Ala55Thr Uncertain significance ★ ⚠ same type
- FYN p.Arg123Cys Uncertain significance ★ ⚠ same type
- FYN p.Arg161Ter Uncertain significance ★ same type
- FYN p.Arg29Cys Uncertain significance ★ ⚠ same type
- FYN p.Asp8Glu Uncertain significance ★ ⚠ same type
- FYN p.Asp92Asn 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/fyn-p-phe42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown