DIP2A p.Thr848=
c.2544C>T · rs143909470 · VCV708063
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.01%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -4.2 |
| Overall | ||
| CADD | 0.064 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.01%
African / African-American · 760/75,050 alleles
Filtering AF
0.953%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.929%
Overall
0.0659%
1,063/1,613,792 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.01% | 99 |
| Remaining individualsnot grpmax-eligible | 0.0912% | 1,097 |
| Admixed American | 0.0483% | 2,070 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.0177% | 5,646 |
| South Asian | 0.00439% | 22,772 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| East Asian | 0.00223% | 44,886 |
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
- DIP2A
- Protein
- p.Thr848=
- Coding
- c.2544C>T
- MANE Select
- NM_015151
- dbSNP
- rs143909470
- Type
- single nucleotide variant
- Location
- chr21:46549792 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.93
Similar variants
- DIP2A p.Ala676Thr Uncertain significance ★★ ⚠ same type
- DIP2A p.Glu832Lys Uncertain significance ★★ ⚠ same type
- DIP2A p.Pro333= Benign ★★ same type
- DIP2A p.Pro798Leu Benign/Likely benign ★★ ⚠ same type
- DIP2A p.Val1531= Benign ★★ same type
- DIP2A c.1429+2T>G Likely pathogenic ★ same type
- DIP2A c.2395-2A>G Uncertain significance ★ same type
- DIP2A p.Ala1017Thr 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/dip2a-p-thr848 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown