Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.84%, 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 0.96 | GERP -0.34, phastCons 1 |
| Overall | ||
| CADD | 6.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.84%
African / African-American · 1,380/74,974 alleles
Filtering AF
1.76%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.73%
Overall
0.0946%
1,525/1,612,590 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.84% | 54 |
| Admixed American | 0.124% | 809 |
| Remaining individualsnot grpmax-eligible | 0.0785% | 1,274 |
| Middle Eastern | 0.0661% | 1,514 |
| European (non-Finnish) | 0.00153% | 65,511 |
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
- CARF
- Protein
- p.Gly506=
- Coding
- c.1518G>A
- MANE Select
- NM_024744
- dbSNP
- rs6721180
- Type
- single nucleotide variant
- Location
- chr2:202977292 (GRCh38)
- Gene constraint
- LOEUF 0.782 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 56.59
Similar variants
- CARF p.Gln640Pro Uncertain significance ★★ ⚠ same type
- CARF c.*377G>A Benign ★★ same type
- CARF p.Pro108Ser Likely benign ★★ same type
- CARF p.Pro454= Benign ★★ same type
- CARF p.Thr725Ala Benign ★★ same type
- CARF p.Val157Ala Likely benign ★★ same type
- CARF p.Ala629Val Uncertain significance ★ ⚠ same type
- CARF p.Arg142Trp 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/carf-p-gly506 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown