DCC c.3130+17A>G
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.172%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +17 | near-intronic (+17 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -3.7 |
| Non-coding constraint | Z 0.52 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 0.018 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.172%
African / African-American · 125/72,862 alleles
Filtering AF
0.147%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.138%
Overall
0.0117%
168/1,437,288 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.172% | 583 |
| Middle Eastern | 0.0869% | 1,151 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0454% | 2,202 |
| Remaining individualsnot grpmax-eligible | 0.0264% | 3,793 |
| Admixed American | 0.00167% | 59,780 |
| South Asian | 0.00113% | 88,142 |
| European (non-Finnish) | 0.000787% | 127,016 |
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
- DCC
- Coding
- c.3130+17A>G
- MANE Select
- NM_005215
- Type
- single nucleotide variant
- Location
- chr18:53410663 (GRCh38)
- Gene constraint
- LOEUF 0.414 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 68.60 · 9 PDB
Similar variants
- DCC p.Arg1021Ter Pathogenic ★★ same type
- DCC p.Arg1025Ter Pathogenic/Likely pathogenic ★★ same type
- DCC p.Arg275Ter Pathogenic ★★ same type
- DCC p.Arg879Ter Pathogenic/Likely pathogenic ★★ same type
- DCC c.3620-2A>G Uncertain significance ★★ same type
- DCC p.Arg597Gln Uncertain significance ★★ ⚠ same type
- DCC p.Gly1294Arg Uncertain significance ★★ ⚠ same type
- DCC p.Gly55Arg 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/dcc-c-3130-plus-17a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown