ATP2B4 p.Asn656=
c.1968T>C · rs75360548 · VCV703856
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 5.59%, afr) — 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 | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.7 | GERP -3.8 |
| Overall | ||
| CADD | 4.162 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.59%
African / African-American · 4,193/75,018 alleles
Filtering AF
5.45%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.39%
Overall
0.298%
4,802/1,614,026 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.59% | 18 |
| Remaining individualsnot grpmax-eligible | 0.347% | 288 |
| Admixed American | 0.28% | 357 |
| Middle Eastern | 0.247% | 404 |
| South Asian | 0.022% | 4,553 |
| European (non-Finnish) | 0.0159% | 6,276 |
| East Asian | 0.00223% | 44,874 |
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
- ATP2B4
- Protein
- p.Asn656=
- Coding
- c.1968T>C
- MANE Select
- NM_001684
- dbSNP
- rs75360548
- Type
- single nucleotide variant
- Location
- chr1:203711045 (GRCh38)
- Gene constraint
- LOEUF 0.44 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.71 · 2 PDB
Similar variants
- ATP2B4 p.Arg554Cys Uncertain significance ★★ same type
- ATP2B4 p.Arg624Cys Uncertain significance ★★ same type
- ATP2B4 p.Arg732Cys Uncertain significance ★★ same type
- ATP2B4 p.Arg993Gly Uncertain significance ★★ same type
- ATP2B4 p.Asn851Ser Uncertain significance ★★ same type
- ATP2B4 p.Asp333Gly Uncertain significance ★★ same type
- ATP2B4 p.Asp502Asn Uncertain significance ★★ same type
- ATP2B4 p.Gly634Arg 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/atp2b4-p-asn656 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown