DIP2B p.Ser544=
c.1632G>A · rs115245528 · VCV789047
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.57%, 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 -0.43 | GERP -4.9, phastCons 0.008 |
| Overall | ||
| CADD | 6.034 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.57%
African / African-American · 1,927/74,980 alleles
Filtering AF
2.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.44%
Overall
0.133%
2,152/1,613,962 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.57% | 39 |
| Remaining individualsnot grpmax-eligible | 0.154% | 651 |
| Admixed American | 0.145% | 690 |
| Middle Eastern | 0.132% | 758 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,802 |
| South Asian | 0.00549% | 18,215 |
| European (non-Finnish) | 0.00229% | 43,702 |
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
- DIP2B
- Protein
- p.Ser544=
- Coding
- c.1632G>A
- MANE Select
- NM_173602
- dbSNP
- rs115245528
- Type
- single nucleotide variant
- Location
- chr12:50691129 (GRCh38)
- Gene constraint
- LOEUF 0.448 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.83
Similar variants
- DIP2B p.Ser544Leu Likely benign ★ ⚠ same residue
- DIP2B p.Asp501Val Uncertain significance ★★ ⚠ same type
- DIP2B p.Cys1071Ser Uncertain significance ★★ ⚠ same type
- DIP2B p.His1027Arg Uncertain significance ★★ ⚠ same type
- DIP2B p.Ile681Val Uncertain significance ★★ ⚠ same type
- DIP2B p.Ile968Thr Uncertain significance ★★ ⚠ same type
- DIP2B p.Ile994Leu Uncertain significance ★★ ⚠ same type
- DIP2B p.Pro244Ala 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/dip2b-p-ser544 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown