BDP1 p.Ile1972=
c.5916C>A · rs35131626 · VCV508602
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.55%, sas) — 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 1 | GERP 2.7, phastCons 0.51 |
| Overall | ||
| CADD | 6.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.55%
South Asian · 5,848/89,328 alleles
Filtering AF
6.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.35%
Overall
2.72%
43,425/1,599,206 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 6.55% | 15 |
| Finnishnot grpmax-eligible | 3.64% | 27 |
| Admixed American | 3.5% | 29 |
| Middle Eastern | 2.81% | 36 |
| Remaining individualsnot grpmax-eligible | 2.55% | 39 |
| European (non-Finnish) | 2.53% | 40 |
| Ashkenazi Jewishnot grpmax-eligible | 2.5% | 40 |
| African / African-American | 1.03% | 97 |
| East Asian | 0.881% | 114 |
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
- BDP1
- Protein
- p.Ile1972=
- Coding
- c.5916C>A
- MANE Select
- NM_018429
- dbSNP
- rs35131626
- Type
- single nucleotide variant
- Location
- chr5:71539065 (GRCh38)
- Gene constraint
- LOEUF 0.683 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 37.23 · 13 PDB
Similar variants
- BDP1 p.Arg880Gly Uncertain significance ★★ ⚠ same type
- BDP1 p.Arg935Ile Uncertain significance ★★ ⚠ same type
- BDP1 p.Asp1875Asn Uncertain significance ★★ ⚠ same type
- BDP1 p.Glu1139Val Uncertain significance ★★ ⚠ same type
- BDP1 p.Ile1035Met Uncertain significance ★★ ⚠ same type
- BDP1 p.Lys1304Glu Uncertain significance ★★ ⚠ same type
- BDP1 p.Lys354Glu Uncertain significance ★★ ⚠ same type
- BDP1 p.Pro1432Leu 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/bdp1-p-ile1972 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown