ALK c.3645+199C>T
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 72.8%, eas) — 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 | ||
| Splice region | donor +199 | deep intronic (+199 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.12 | GERP -1.2 |
| Non-coding constraint | Z 2.96 | 1 kb window · o/e 0.80 · regional · uncalibrated |
| Overall | ||
| CADD | 3.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
72.8%
East Asian · 3,753/5,156 alleles
Filtering AF
70.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 70.1%
Overall
27.7%
42,130/151,992 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 72.8% | 1 |
| Admixed American | 42.7% | 2 |
| South Asian | 41.4% | 2 |
| Amishnot grpmax-eligible | 41% | 2 |
| Finnishnot grpmax-eligible | 32.4% | 3 |
| Remaining individualsnot grpmax-eligible | 27.7% | 4 |
| African / African-American | 24.9% | 4 |
| European (non-Finnish) | 21.4% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 17.1% | 6 |
| Middle Eastern | 13.3% | 8 |
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
- ALK
- Coding
- c.3645+199C>T
- MANE Select
- NM_004304
- dbSNP
- rs4665446
- Type
- single nucleotide variant
- Location
- chr2:29220507 (GRCh38)
- Gene constraint
- LOEUF 0.562 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.26 · 79 PDB
Similar variants
- ALK p.Arg1275Gln Pathogenic ★★ same type
- ALK c.1154+5G>A Uncertain significance ★★ same type
- ALK c.1155-3C>T Uncertain significance ★★ same type
- ALK c.1282+3A>G Uncertain significance ★★ same type
- ALK c.1414+1G>A Uncertain significance ★★ same type
- ALK c.1414+3G>A Uncertain significance ★★ same type
- ALK c.1415-3T>C Uncertain significance ★★ same type
- ALK c.1546+4C>T 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/alk-c-3645-plus-199c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown