HCK c.1C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,283,550)
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 6.5 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 19.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,283,550). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- HCK
- Coding
- c.1C>T
- MANE Select
- NM_002110
- dbSNP
- rs2515888618
- Type
- single nucleotide variant
- Location
- chr20:32052425 (GRCh38)
- Gene constraint
- LOEUF 0.795 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.93 · 42 PDB
Similar variants
- HCK p.Arg123Trp Uncertain significance ★★ ⚠ same type
- HCK p.Glu75Gln Uncertain significance ★★ ⚠ same type
- HCK p.Leu139Val Uncertain significance ★★ ⚠ same type
- HCK p.Ser5Pro Uncertain significance ★★ ⚠ same type
- HCK p.Ala44Thr Benign/Likely benign ★★ same type
- HCK p.Asn64= Benign ★★ same type
- HCK p.Asp231= Benign/Likely benign ★★ same type
- HCK p.Glu110= Likely benign ★★ 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/hck-c-1c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown