APOBEC3H p.Phe107=
c.321C>T · rs112605061 · VCV717866
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.54%, afr)
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 -4.7 | GERP -2.8 |
| Overall | ||
| CADD | 3.007 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.54%
African / African-American · 1,144/74,296 alleles
Filtering AF
1.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.44%
Overall
0.0869%
1,401/1,611,652 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.54% | 65 |
| Remaining individualsnot grpmax-eligible | 0.134% | 744 |
| Admixed American | 0.0955% | 1,047 |
| Middle Eastern | 0.0668% | 1,496 |
| European (non-Finnish) | 0.00907% | 11,022 |
| South Asian | 0.0055% | 18,187 |
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
- APOBEC3H
- Protein
- p.Phe107=
- Coding
- c.321C>T
- MANE Select
- NM_181773
- dbSNP
- rs112605061
- Type
- single nucleotide variant
- Location
- chr22:39101407 (GRCh38)
- Gene constraint
- LOEUF 0.651 · pLI 0.63 (gnomAD)
- Structure
- AlphaFold pLDDT 89.41 · 4 PDB
- Residue 107
- the cmp/dcmp-type deaminase domain; a β-strand
Similar variants
- APOBEC3H p.Arg10Cys Uncertain significance ★ ⚠ same type
- APOBEC3H p.Arg10His Uncertain significance ★ ⚠ same type
- APOBEC3H p.Arg110His Uncertain significance ★ ⚠ same type
- APOBEC3H p.Arg17Cys Uncertain significance ★ ⚠ same type
- APOBEC3H p.Arg17His Uncertain significance ★ ⚠ same type
- APOBEC3H p.Cys116Trp Uncertain significance ★ ⚠ same type
- APOBEC3H p.Glu146Gly Uncertain significance ★ ⚠ same type
- APOBEC3H p.Glu48Gly 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/apobec3h-p-phe107 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown