KIT c.67+90A>G
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 13.1%, 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 | ||
| Splice region | donor +90 | deep intronic (+90 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.054 | GERP -0.14, phastCons 0.011 |
| Overall | ||
| CADD | 4.451 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
13.1%
African / African-American · 9,115/69,638 alleles
Filtering AF
12.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 12.8%
Overall
0.797%
10,608/1,330,778 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 13.1% | 8 |
| Remaining individualsnot grpmax-eligible | 1.01% | 99 |
| Admixed American | 0.965% | 104 |
| Middle Eastern | 0.6% | 167 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0724% | 1,382 |
| South Asian | 0.0509% | 1,964 |
| European (non-Finnish) | 0.0325% | 3,078 |
| Finnishnot grpmax-eligible | 0.00169% | 59,102 |
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
- KIT
- Coding
- c.67+90A>G
- MANE Select
- NM_000222
- dbSNP
- rs72550821
- Type
- single nucleotide variant
- Location
- chr4:54658171 (GRCh38)
- Gene constraint
- LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.52 · 65 PDB
Similar variants
- KIT p.Ala621Thr Pathogenic/Likely pathogenic ★★ same type
- KIT p.Asp816His Pathogenic ★★ same type
- KIT p.Asp820Tyr Pathogenic ★★ same type
- KIT p.Gln190Ter Pathogenic ★★ same type
- KIT p.Leu576Pro Pathogenic/Likely pathogenic ★★ same type
- KIT p.Lys642Glu Pathogenic ★★ same type
- KIT p.Trp557Arg Pathogenic/Likely pathogenic ★★ same type
- KIT p.Val559Ala Pathogenic/Likely pathogenic ★★ 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/kit-c-67-plus-90a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown