DIP2C p.Cys1004=
c.3012C>T · rs79727010 · VCV773532
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.85%, 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 0.036 | GERP -3.2, phastCons 0.048 |
| Overall | ||
| CADD | 7.699 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.85%
African / African-American · 2,888/75,022 alleles
Filtering AF
3.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.68%
Overall
0.339%
5,459/1,609,262 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.85% | 26 |
| Middle Eastern | 1.32% | 76 |
| Admixed American | 0.763% | 131 |
| Remaining individualsnot grpmax-eligible | 0.609% | 164 |
| Ashkenazi Jewishnot grpmax-eligible | 0.368% | 271 |
| European (non-Finnish) | 0.127% | 789 |
| South Asian | 0.0494% | 2,023 |
| Finnishnot grpmax-eligible | 0.0066% | 15,156 |
| East Asian | 0.00223% | 44,838 |
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
- DIP2C
- Protein
- p.Cys1004=
- Coding
- c.3012C>T
- MANE Select
- NM_014974
- dbSNP
- rs79727010
- Type
- single nucleotide variant
- Location
- chr10:349428 (GRCh38)
- Gene constraint
- LOEUF 0.235 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.64
Similar variants
- DIP2C p.Ala1066Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1066Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1101Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1155Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala1466Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala193Val Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala422Thr Uncertain significance ★★ ⚠ same type
- DIP2C p.Ala71Thr 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/dip2c-p-cys1004 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown