BLTP3B p.Ser688=
c.2064T>C · rs73388024 · VCV716330
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 5.26%, afr) — too common for a highly-penetrant pathogenic allele
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 1.1 | GERP -1.6, phastCons 0.99 |
| Overall | ||
| CADD | 5.947 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.26%
African / African-American · 3,946/75,020 alleles
Filtering AF
5.12%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.07%
Overall
0.278%
4,481/1,614,052 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.26% | 19 |
| Admixed American | 0.37% | 270 |
| Remaining individualsnot grpmax-eligible | 0.363% | 275 |
| Middle Eastern | 0.181% | 551 |
| South Asian | 0.0121% | 8,278 |
| European (non-Finnish) | 0.00542% | 18,437 |
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
- BLTP3B
- Protein
- p.Ser688=
- Coding
- c.2064T>C
- MANE Select
- NM_015054
- dbSNP
- rs73388024
- Type
- single nucleotide variant
- Location
- chr12:100059213 (GRCh38)
- Structure
- AlphaFold pLDDT 67.53
Similar variants
- BLTP3B p.Leu491= Benign ★★ same type
- BLTP3B p.Ala109Val Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala1162Thr Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala1272Ser Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala231Ser Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala231Thr Uncertain significance ★ ⚠ same type
- BLTP3B p.Ala257Gly Uncertain significance ★ same type
- BLTP3B p.Ala66Thr 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/bltp3b-p-ser688 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown