ANK1 c.3115+9G>C
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.989%, afr)
Conditions
1
hereditary spherocytosis type 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -2.8 |
| Non-coding constraint | Z 3.77 | 1 kb window · o/e 0.74 · regional · uncalibrated |
| Overall | ||
| CADD | 0.769 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.989%
African / African-American · 742/75,048 alleles
Filtering AF
0.93%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.906%
Overall
0.0512%
826/1,614,064 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.989% | 101 |
| Admixed American | 0.075% | 1,334 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,083 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.000593% | 168,576 |
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
- ANK1
- Coding
- c.3115+9G>C
- MANE Select
- NM_000037
- dbSNP
- rs150850103
- Type
- single nucleotide variant
- Location
- chr8:41695168 (GRCh38)
- Gene constraint
- LOEUF 0.299 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.64 · 21 PDB
Disease context
hereditary spherocytosis type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hereditary spherocytosis (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- All ages
- Prevalence
- 1-5 / 10 000 (Germany)
Similar variants
- ANK1 c.1305+1G>A Pathogenic ★★ same condition
- ANK1 c.1405-9G>A Pathogenic/Likely pathogenic ★★ same condition
- ANK1 c.1702-2A>G Pathogenic/Likely pathogenic ★★ same condition
- ANK1 c.1801-17G>A Pathogenic/Likely pathogenic ★★ same condition
- ANK1 c.2296-1G>A Likely pathogenic ★★ same condition
- ANK1 c.2296-2A>G Pathogenic/Likely pathogenic ★★ same condition
- ANK1 c.2389-2A>G Likely pathogenic ★★ same condition
- ANK1 c.2462-2A>G Pathogenic ★★ same condition
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/ank1-c-3115-plus-9g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown