B9D2 p.Phe127=
c.381C>T · rs372769452 · VCV779810
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0362%, 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 -4.8 | GERP -2.7 |
| Overall | ||
| CADD | 5.967 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0362%
South Asian · 33/91,092 alleles
Filtering AF
0.0265%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0231%
Overall
0.00273%
44/1,613,798 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0362% | 2,760 |
| East Asian | 0.00668% | 14,962 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,241 |
| Admixed American | 0.00167% | 60,006 |
| African / African-American | 0.00133% | 74,930 |
| European (non-Finnish) | 0.000339% | 294,996 |
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
- B9D2
- Protein
- p.Phe127=
- Coding
- c.381C>T
- MANE Select
- NM_030578
- dbSNP
- rs372769452
- Type
- single nucleotide variant
- Location
- chr19:41354847 (GRCh38)
- Gene constraint
- LOEUF 1.518 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.79
Similar variants
- B9D2 p.Gly155Ser Pathogenic/Likely pathogenic ★★ same type
- B9D2 p.Pro74Ser Pathogenic/Likely pathogenic ★★ same type
- B9D2 p.Ser101Arg Pathogenic/Likely pathogenic ★★ same type
- B9D2 p.Ala31Glu Uncertain significance ★★ ⚠ same type
- B9D2 p.Arg120Gln Uncertain significance ★★ ⚠ same type
- B9D2 p.Arg166Cys Uncertain significance ★★ ⚠ same type
- B9D2 p.Arg88Cys Uncertain significance ★★ ⚠ same type
- B9D2 p.Gln50His 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/b9d2-p-phe127 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown