BECN1 p.Pro350=
c.1050G>A · rs369643771 · VCV3133659
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0841%, sas)
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 -16 | GERP -5.5 |
| Overall | ||
| CADD | 1.339 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0841%
South Asian · 76/90,404 alleles
Filtering AF
0.0689%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0633%
Overall
0.00627%
101/1,610,608 alleles · ultra-rare
exomes 89/1,458,310 · genomes 12/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0841% | 1,190 |
| East Asian | 0.0134% | 7,478 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,467 |
| Admixed American | 0.0034% | 29,438 |
| African / African-American | 0.00268% | 37,364 |
| European (non-Finnish) | 0.000848% | 117,902 |
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
- BECN1
- Protein
- p.Pro350=
- Coding
- c.1050G>A
- MANE Select
- NM_001313998
- dbSNP
- rs369643771
- Type
- single nucleotide variant
- Location
- chr17:42811789 (GRCh38)
- Gene constraint
- LOEUF 0.33 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.37 · 33 PDB
- Residue 350
- the 'evolutionary conserved domain (ecd)' region; a β-strand
Similar variants
- BECN1 c.980+9T>C Benign ★★ same type
- BECN1 c.-2-2A>G Uncertain significance ★ same type
- BECN1 p.Arg255His Uncertain significance ★ ⚠ same type
- BECN1 p.Arg329Gln Uncertain significance ★ ⚠ same type
- BECN1 p.Arg80Cys Uncertain significance ★ ⚠ same type
- BECN1 p.Arg80Leu Uncertain significance ★ ⚠ same type
- BECN1 p.Asn286Asp Uncertain significance ★ ⚠ same type
- BECN1 p.Gln224Glu 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/becn1-p-pro350 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown