BLTP1 p.Gln2929=
c.8787G>A · rs28651726 · VCV1229405
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 12.8%, 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. | ||
| REVEL | 0.493 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -5.2 |
| Overall | ||
| CADD | 0.538 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
12.8%
African / African-American · 9,590/74,980 alleles
Filtering AF
12.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 12.5%
Overall
0.69%
11,142/1,613,948 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 12.8% | 8 |
| Remaining individualsnot grpmax-eligible | 0.875% | 114 |
| Admixed American | 0.82% | 122 |
| Middle Eastern | 0.71% | 141 |
| Ashkenazi Jewishnot grpmax-eligible | 0.503% | 199 |
| South Asian | 0.0285% | 3,503 |
| European (non-Finnish) | 0.025% | 4,000 |
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
- BLTP1
- Protein
- p.Gln2929=
- Coding
- c.8787G>A
- MANE Select
- NM_001384125
- dbSNP
- rs28651726
- Type
- single nucleotide variant
- Location
- chr4:122279970 (GRCh38)
- Residue 2929
- the 'disordered' region; a UniProt-annotated variant site (in alkkucs)
Similar variants
- BLTP1 p.Arg968Cys Likely pathogenic ★★ ⚠ same type
- BLTP1 c.1498+4A>G Uncertain significance ★★ same type
- BLTP1 p.Ala2332Thr Uncertain significance ★★ ⚠ same type
- BLTP1 p.Arg1317His Uncertain significance ★★ same type
- BLTP1 p.Arg1791Lys Uncertain significance ★★ ⚠ same type
- BLTP1 p.Arg2095His Uncertain significance ★★ same type
- BLTP1 p.Arg2279Cys Uncertain significance ★★ same type
- BLTP1 p.Arg3665Gln 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/bltp1-p-gln2929 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown