C2CD3 c.3517+63G>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 47.9%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| Splice region | donor +63 | deep intronic (+63 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Non-coding constraint | Z 1.25 | 1 kb window · o/e 0.89 · regional · uncalibrated |
| Overall | ||
| CADD | 2.508 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
47.9%
African / African-American · 34,057/71,070 alleles
Filtering AF
47.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 47.3%
Overall
29.3%
430,665/1,469,656 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 47.9% | 2 |
| Admixed American | 37.6% | 3 |
| Middle Eastern | 36.6% | 3 |
| Amishnot grpmax-eligible | 31.4% | 3 |
| Remaining individualsnot grpmax-eligible | 29.2% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 28.7% | 3 |
| European (non-Finnish) | 28.5% | 4 |
| South Asian | 26% | 4 |
| Finnishnot grpmax-eligible | 25.9% | 4 |
| East Asian | 18.7% | 5 |
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
- C2CD3
- Coding
- c.3517+63G>A
- MANE Select
- NM_001286577
- dbSNP
- rs1790400
- Type
- single nucleotide variant
- Location
- chr11:74092353 (GRCh38)
- Gene constraint
- LOEUF 0.637 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.65
Similar variants
- C2CD3 c.3911-2A>T Pathogenic/Likely pathogenic ★★ same type
- C2CD3 p.Arg621Ter Pathogenic/Likely pathogenic ★★ same type
- C2CD3 p.Arg666Ter Pathogenic ★★ same type
- C2CD3 p.Arg768Ter Pathogenic/Likely pathogenic ★★ same type
- C2CD3 p.Tyr173Ter Pathogenic/Likely pathogenic ★★ same type
- C2CD3 c.2085+5G>A Uncertain significance ★★ same type
- C2CD3 c.4951+6C>T Uncertain significance ★★ same type
- C2CD3 c.5495+4A>G 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/c2cd3-c-3517-plus-63g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown