ANKRD52 p.Thr620=
c.1860C>T · VCV3873731
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0233%, amr)
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 -6.8 | GERP -3.7 |
| Overall | ||
| CADD | 9.161 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0233%
Admixed American · 14/60,014 alleles
Filtering AF
0.0141%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0112%
Overall
0.00564%
91/1,613,814 alleles · ultra-rare
exomes 81/1,461,570 · genomes 10/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0233% | 4,287 |
| European (non-Finnish) | 0.00559% | 17,877 |
| African / African-American | 0.00534% | 18,736 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,821 |
| South Asian | 0.00439% | 22,773 |
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
- ANKRD52
- Protein
- p.Thr620=
- Coding
- c.1860C>T
- MANE Select
- NM_173595
- Type
- single nucleotide variant
- Location
- chr12:56248141 (GRCh38)
- Gene constraint
- LOEUF 0.122 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.71
Similar variants
- ANKRD52 c.694-3C>T Benign ★★ same type
- ANKRD52 p.Asn466= Benign ★★ same type
- ANKRD52 p.Ala102Ser Uncertain significance ★ ⚠ same type
- ANKRD52 p.Ala1041Val Uncertain significance ★ ⚠ same type
- ANKRD52 p.Ala1043Thr Uncertain significance ★ ⚠ same type
- ANKRD52 p.Ala1051Thr Uncertain significance ★ ⚠ same type
- ANKRD52 p.Ala1067Thr Uncertain significance ★ ⚠ same type
- ANKRD52 p.Ala215Val 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/ankrd52-p-thr620 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown