CARNMT1 p.Asp295=
c.885T>C · rs12380147 · VCV782145
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.933%, 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 4 | GERP -0.85, phastCons 1 |
| Overall | ||
| CADD | 7.858 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.933%
Admixed American · 491/52,634 alleles
Filtering AF
0.865%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.838%
Overall
0.584%
9,261/1,585,244 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.933% | 107 |
| European (non-Finnish) | 0.676% | 148 |
| Remaining individualsnot grpmax-eligible | 0.473% | 211 |
| Amishnot grpmax-eligible | 0.439% | 228 |
| Finnishnot grpmax-eligible | 0.436% | 229 |
| Ashkenazi Jewishnot grpmax-eligible | 0.202% | 495 |
| South Asian | 0.179% | 558 |
| Middle Eastern | 0.169% | 592 |
| African / African-American | 0.109% | 918 |
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
- CARNMT1
- Protein
- p.Asp295=
- Coding
- c.885T>C
- MANE Select
- NM_152420
- dbSNP
- rs12380147
- Type
- single nucleotide variant
- Location
- chr9:74998623 (GRCh38)
- Gene constraint
- LOEUF 1.157 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.52 · 3 PDB
- Residue 295
- a binding site
Similar variants
- CARNMT1 p.Ala49Val Uncertain significance ★ ⚠ same type
- CARNMT1 p.Arg13Pro Uncertain significance ★ ⚠ same type
- CARNMT1 p.Arg63His Uncertain significance ★ ⚠ same type
- CARNMT1 p.Arg83Gln Uncertain significance ★ ⚠ same type
- CARNMT1 p.Asn249His Uncertain significance ★ ⚠ same type
- CARNMT1 p.Asn288Asp Uncertain significance ★ ⚠ same type
- CARNMT1 p.Asn353Ser Uncertain significance ★ ⚠ same type
- CARNMT1 p.Asp117Glu 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/carnmt1-p-asp295 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown