ANO6 c.70+252C>T
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 29.8%, 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 +252 | deep intronic (+252 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.066 | GERP -1 |
| Non-coding constraint | Z 2.52 | 1 kb window · o/e 0.86 · regional · uncalibrated |
| Overall | ||
| CADD | 4.887 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
29.8%
East Asian · 1,531/5,138 alleles
Filtering AF
28.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 28.1%
Overall
5.86%
8,929/152,262 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 29.8% | 3 |
| South Asian | 14.9% | 7 |
| Middle Eastern | 10.2% | 10 |
| Finnishnot grpmax-eligible | 7.04% | 14 |
| Remaining individualsnot grpmax-eligible | 6.29% | 16 |
| European (non-Finnish) | 5.96% | 17 |
| Ashkenazi Jewishnot grpmax-eligible | 5.01% | 20 |
| Admixed American | 4.81% | 21 |
| Amishnot grpmax-eligible | 2.53% | 40 |
| African / African-American | 1.87% | 53 |
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
- ANO6
- Coding
- c.70+252C>T
- MANE Select
- NM_001025356
- dbSNP
- rs11612203
- Type
- single nucleotide variant
- Location
- chr12:45216643 (GRCh38)
- Gene constraint
- LOEUF 1.02 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.00
Similar variants
- ANO6 c.1387-1G>T Pathogenic ★★ same type
- ANO6 p.Arg253Cys Uncertain significance ★★ ⚠ same type
- ANO6 p.Arg253His Uncertain significance ★★ ⚠ same type
- ANO6 p.Arg276Gln Uncertain significance ★★ ⚠ same type
- ANO6 p.Arg399Cys Uncertain significance ★★ same type
- ANO6 p.Arg635Gln Uncertain significance ★★ ⚠ same type
- ANO6 p.Arg648Leu Uncertain significance ★★ ⚠ same type
- ANO6 p.Arg862Cys 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/ano6-c-70-plus-252c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown