CMYA5 p.Asp3328=
c.9984C>T · rs140841478 · VCV787036
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.15%, 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 1.2 | GERP -3.8, phastCons 1 |
| Overall | ||
| CADD | 2.783 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.15%
African / African-American · 866/75,012 alleles
Filtering AF
1.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.07%
Overall
0.0614%
991/1,613,882 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.15% | 87 |
| Remaining individualsnot grpmax-eligible | 0.088% | 1,136 |
| Admixed American | 0.0767% | 1,304 |
| Middle Eastern | 0.033% | 3,031 |
| East Asian | 0.0245% | 4,080 |
| South Asian | 0.0011% | 91,076 |
| European (non-Finnish) | 0.000848% | 117,987 |
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
- CMYA5
- Protein
- p.Asp3328=
- Coding
- c.9984C>T
- MANE Select
- NM_153610
- dbSNP
- rs140841478
- Type
- single nucleotide variant
- Location
- chr5:79738749 (GRCh38)
- Gene constraint
- LOEUF 0.807 · pLI <0.01 (gnomAD)
- Residue 3328
- the 'required for ryr2 clustering' region
Similar variants
- CMYA5 p.Asp3328Asn Uncertain significance ★ ⚠ same residue
- CMYA5 p.Gln1229His Uncertain significance ★★ ⚠ same type
- CMYA5 p.Pro1256Leu Uncertain significance ★★ ⚠ same type
- CMYA5 p.Ala2958Ser Likely benign ★★ same type
- CMYA5 p.Arg147Gln Benign ★★ same type
- CMYA5 p.Asp3147Tyr Benign/Likely benign ★★ same type
- CMYA5 p.Asp53Glu Likely benign ★★ same type
- CMYA5 p.Asp836= Benign ★★ 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/cmya5-p-asp3328 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown