LYN p.Lys233=
c.699G>A · rs2227980 · VCV1168285
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 40.5%, afr) — too common for a highly-penetrant pathogenic allele
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 3.8 | GERP 0.74, phastCons 1 |
| Overall | ||
| CADD | 9.598 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
40.5%
African / African-American · 30,327/74,908 alleles
Filtering AF
40.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 39.9%
Overall
4.89%
78,987/1,613,918 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 40.5% | 2 |
| Admixed American | 5.92% | 17 |
| Remaining individualsnot grpmax-eligible | 5.34% | 19 |
| Middle Eastern | 4.34% | 23 |
| East Asian | 3.14% | 32 |
| European (non-Finnish) | 3.09% | 32 |
| South Asian | 2.3% | 43 |
| Amishnot grpmax-eligible | 1.97% | 51 |
| Finnishnot grpmax-eligible | 1.9% | 53 |
| Ashkenazi Jewishnot grpmax-eligible | 0.871% | 115 |
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
- LYN
- Protein
- p.Lys233=
- Coding
- c.699G>A
- MANE Select
- NM_002350
- dbSNP
- rs2227980
- Type
- single nucleotide variant
- Location
- chr8:55953893 (GRCh38)
- Gene constraint
- LOEUF 0.282 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.44 · 6 PDB
Similar variants
- LYN p.Ala150Thr Uncertain significance ★★ ⚠ same type
- LYN p.Ala70Thr Uncertain significance ★★ ⚠ same type
- LYN p.Arg360Trp Uncertain significance ★★ ⚠ same type
- LYN p.Glu47Asp Uncertain significance ★★ ⚠ same type
- LYN p.Ile227Val Uncertain significance ★★ ⚠ same type
- LYN p.Ser333Asn Uncertain significance ★★ same type
- LYN p.Thr30Ala Uncertain significance ★★ ⚠ same type
- LYN p.Val45Ile 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/lyn-p-lys233 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown