Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.22%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.47 | donor loss, 6 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP -3.9, phastCons 1 |
| Overall | ||
| CADD | 11.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.22%
African / African-American · 2,413/74,992 alleles
Filtering AF
3.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.07%
Overall
0.168%
2,715/1,614,012 alleles · low-frequency
exomes 1,305/1,461,802 · genomes 1,410/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.22% | 31 |
| Admixed American | 0.218% | 458 |
| Remaining individualsnot grpmax-eligible | 0.202% | 496 |
| Middle Eastern | 0.066% | 1,516 |
| South Asian | 0.00549% | 18,215 |
| European (non-Finnish) | 0.00305% | 32,777 |
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
- PSMC3IP
- Protein
- p.Ser82=
- Coding
- c.246T>C
- MANE Select
- NM_016556
- dbSNP
- rs9903184
- Type
- single nucleotide variant
- Location
- chr17:42574190 (GRCh38)
- Gene constraint
- LOEUF 0.981 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.45
Similar variants
- PSMC3IP p.Glu160Lys Uncertain significance ★★ ⚠ same type
- PSMC3IP c.136-10C>T Benign ★★ same type
- PSMC3IP c.225+79G>A Benign ★★ same type
- PSMC3IP c.225+89C>T Likely benign ★★ same type
- PSMC3IP c.337+88C>T Benign ★★ same type
- PSMC3IP c.338-147T>C Benign ★★ same type
- PSMC3IP c.338-158G>A Benign ★★ same type
- PSMC3IP c.338-15C>G 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/psmc3ip-p-ser82 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown