Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 36.8%, eas) — 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 2.9 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 9.692 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
36.8%
East Asian · 16,307/44,278 alleles
Filtering AF
36.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 36.2%
Overall
10.7%
169,552/1,587,854 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 36.8% | 3 |
| South Asian | 18.8% | 5 |
| Remaining individualsnot grpmax-eligible | 11.3% | 9 |
| African / African-American | 10.3% | 10 |
| European (non-Finnish) | 9.47% | 11 |
| Amishnot grpmax-eligible | 9.21% | 11 |
| Admixed American | 8.07% | 12 |
| Ashkenazi Jewishnot grpmax-eligible | 7.39% | 14 |
| Finnishnot grpmax-eligible | 7.21% | 14 |
| Middle Eastern | 7.04% | 14 |
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
- CDIN1
- Protein
- p.Tyr141=
- Coding
- c.423T>C
- MANE Select
- NM_001321759
- dbSNP
- rs7183415
- Type
- single nucleotide variant
- Location
- chr15:36691761 (GRCh38)
- Gene constraint
- LOEUF 0.931 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.59
Similar variants
- CDIN1 p.Ala100Ser Uncertain significance ★★ ⚠ same type
- CDIN1 p.Arg101Trp Uncertain significance ★★ ⚠ same type
- CDIN1 p.Glu66Ala Uncertain significance ★★ ⚠ same type
- CDIN1 p.Pro33Leu Uncertain significance ★★ ⚠ same type
- CDIN1 p.Thr271Lys Uncertain significance ★★ ⚠ same type
- CDIN1 p.Tyr236Cys Uncertain significance ★★ ⚠ same type
- CDIN1 p.Val203Phe Uncertain significance ★★ ⚠ same type
- CDIN1 c.148-19G>T Benign/Likely benign ★★ 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/cdin1-p-tyr141 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown