ITK c.985+241C>A
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 97.7%, 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 +241 | deep intronic (+241 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.7 | GERP -0.3, phastCons 0.001 |
| Non-coding constraint | Z 1.31 | 1 kb window · o/e 0.91 · regional · uncalibrated |
| Overall | ||
| CADD | 0.386 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
97.7%
East Asian · 31,549/32,292 alleles
Filtering AF
96.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 96.4%
Overall
74.6%
419,178/561,766 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 97.7% | 1 |
| South Asian | 82.3% | 1 |
| Admixed American | 80.6% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 79.8% | 1 |
| Middle Eastern | 76% | 1 |
| Remaining individualsnot grpmax-eligible | 76% | 1 |
| European (non-Finnish) | 71.8% | 1 |
| Finnishnot grpmax-eligible | 69.3% | 1 |
| African / African-American | 66.9% | 1 |
| Amishnot grpmax-eligible | 63.5% | 2 |
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
- ITK
- Coding
- c.985+241C>A
- MANE Select
- NM_005546
- dbSNP
- rs30119
- Type
- single nucleotide variant
- Location
- chr5:157240436 (GRCh38)
- Gene constraint
- LOEUF 0.644 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.82 · 37 PDB
Similar variants
- ITK p.Arg562Ter Pathogenic/Likely pathogenic ★★ same type
- ITK c.851+5G>A Uncertain significance ★★ same type
- ITK p.Ala191Thr Uncertain significance ★★ ⚠ same type
- ITK p.Ala261Thr Uncertain significance ★★ ⚠ same type
- ITK p.Ala308Ser Uncertain significance ★★ ⚠ same type
- ITK p.Ala345Val Uncertain significance ★★ ⚠ same type
- ITK p.Ala471Thr Uncertain significance ★★ ⚠ same type
- ITK p.Ala525Thr 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/itk-c-985-plus-241c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown