Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 10.5%, 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 4.2 | GERP 4.7, phastCons 1 |
| Overall | ||
| CADD | 7.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.5%
African / African-American · 7,899/74,978 alleles
Filtering AF
10.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.3%
Overall
0.559%
9,013/1,613,020 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 10.5% | 9 |
| Admixed American | 0.74% | 135 |
| Remaining individualsnot grpmax-eligible | 0.696% | 144 |
| Middle Eastern | 0.281% | 356 |
| Ashkenazi Jewishnot grpmax-eligible | 0.145% | 688 |
| South Asian | 0.0362% | 2,759 |
| European (non-Finnish) | 0.012% | 8,303 |
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
- BPTF
- Protein
- p.Leu757=
- Coding
- c.2271G>A
- MANE Select
- NM_182641
- dbSNP
- rs7214985
- Type
- single nucleotide variant
- Location
- chr17:67893585 (GRCh38)
- Gene constraint
- LOEUF 0.09 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 757
- the 'disordered' region
Similar variants
- BPTF p.Arg1322Ter Pathogenic/Likely pathogenic ★★ same type
- BPTF p.Arg1738Ter Pathogenic/Likely pathogenic ★★ same type
- BPTF p.Arg2858Ter Pathogenic ★★ same type
- BPTF p.Arg841Ter Pathogenic ★★ same type
- BPTF c.1864+562A>T Uncertain significance ★★ same type
- BPTF c.1865-5651C>G Uncertain significance ★★ ⚠ same type
- BPTF p.Ala1197Val Uncertain significance ★★ ⚠ same type
- BPTF p.Ala1252Val 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/bptf-p-leu757 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown