Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.88%, 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 0.049 | GERP -3.2, phastCons 0.83 |
| Overall | ||
| CADD | 5.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.88%
African / African-American · 2,910/74,924 alleles
Filtering AF
3.77%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.72%
Overall
0.201%
3,248/1,613,150 alleles · low-frequency
exomes 1,670/1,461,080 · genomes 1,578/152,070 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.88% | 26 |
| Remaining individualsnot grpmax-eligible | 0.232% | 431 |
| Middle Eastern | 0.182% | 551 |
| Admixed American | 0.167% | 600 |
| South Asian | 0.00879% | 11,381 |
| European (non-Finnish) | 0.00619% | 16,161 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,598 |
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
- CARMIL2
- Protein
- p.Pro1313=
- Coding
- c.3939T>C
- MANE Select
- NM_001013838
- dbSNP
- rs8044797
- Type
- single nucleotide variant
- Location
- chr16:67656548 (GRCh38)
- Gene constraint
- LOEUF 0.701 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.50
- Residue 1313
- the 'disordered' region; a UniProt-annotated variant site (in imd58; no detectable protein expression in patient's leukocytes; no effect on homodimerization)
Similar variants
- CARMIL2 c.1334+1G>T Likely pathogenic ★★ same type
- CARMIL2 c.2313+1G>A Likely pathogenic ★★ same type
- CARMIL2 c.871+1G>T Pathogenic ★★ same type
- CARMIL2 c.958+1G>A Likely pathogenic ★★ same type
- CARMIL2 p.Arg174Ter Pathogenic/Likely pathogenic ★★ same type
- CARMIL2 p.Asn530Lys Pathogenic/Likely pathogenic ★★ same type
- CARMIL2 p.Gln1379Ter Pathogenic/Likely pathogenic ★★ same type
- CARMIL2 p.Ser370Ter Pathogenic ★★ 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/carmil2-p-pro1313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown