BLTP2 p.Tyr954=
c.2862T>C · rs114672989 · VCV768862
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 5.23%, 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 3.1 | GERP 0.88, phastCons 1 |
| Overall | ||
| CADD | 8.008 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.23%
African / African-American · 3,922/75,026 alleles
Filtering AF
5.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.04%
Overall
0.277%
4,466/1,614,172 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.23% | 19 |
| Admixed American | 0.471% | 212 |
| Remaining individualsnot grpmax-eligible | 0.339% | 295 |
| Middle Eastern | 0.165% | 606 |
| South Asian | 0.00549% | 18,217 |
| European (non-Finnish) | 0.00288% | 34,707 |
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
- BLTP2
- Protein
- p.Tyr954=
- Coding
- c.2862T>C
- MANE Select
- NM_014680
- dbSNP
- rs114672989
- Type
- single nucleotide variant
- Location
- chr17:28634725 (GRCh38)
- Structure
- AlphaFold pLDDT 71.37
Similar variants
- BLTP2 p.Ala1395Ser Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala1564Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala1826Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala248Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala324Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala393Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala539Thr Uncertain significance ★ ⚠ same type
- BLTP2 p.Ala694Gly 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/bltp2-p-tyr954 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown