BLTP1 p.Ser4722=
c.14166A>G · rs76135502 · VCV2655069
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.119%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.035 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.20 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -3 | GERP -8.4 |
| Overall | ||
| CADD | 0.583 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.119%
European (non-Finnish) · 1,400/1,179,638 alleles
Filtering AF
0.113%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.111%
Overall
0.0935%
1,509/1,613,736 alleles · rare
exomes 1,413/1,461,434 · genomes 96/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.119% | 843 |
| Remaining individualsnot grpmax-eligible | 0.0672% | 1,488 |
| South Asian | 0.0307% | 3,253 |
| Admixed American | 0.0283% | 3,530 |
| African / African-American | 0.0267% | 3,752 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,602 |
| Finnishnot grpmax-eligible | 0.00156% | 64,042 |
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.Ser4722=
- Coding
- c.14166A>G
- MANE Select
- NM_001384125
- dbSNP
- rs76135502
- Type
- single nucleotide variant
- Location
- chr4:122352956 (GRCh38)
- Residue 4722
- 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-ser4722 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown