Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 8.85%, afr) — 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 | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.46 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.33 | GERP -3.4, phastCons 1 |
| Overall | ||
| CADD | 8.333 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.85%
African / African-American · 6,461/73,040 alleles
Filtering AF
8.67%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.59%
Overall
0.467%
7,362/1,577,530 alleles · common
exomes 3,589/1,425,422 · genomes 3,773/152,108 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.85% | 11 |
| Middle Eastern | 0.752% | 133 |
| Remaining individualsnot grpmax-eligible | 0.644% | 155 |
| Admixed American | 0.561% | 178 |
| South Asian | 0.0321% | 3,114 |
| European (non-Finnish) | 0.0126% | 7,937 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00737% | 13,570 |
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
- MAP1B
- Protein
- p.Ile171=
- Coding
- c.513C>T
- MANE Select
- NM_005909
- dbSNP
- rs2227915
- Type
- single nucleotide variant
- Location
- chr5:72193868 (GRCh38)
- Gene constraint
- LOEUF 0.105 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.18
Similar variants
- MAP1B p.Arg1664Ter Pathogenic/Likely pathogenic ★★ same type
- MAP1B p.Arg2140Ter Pathogenic ★★ same type
- MAP1B p.Arg303Ter Pathogenic/Likely pathogenic ★★ same type
- MAP1B p.Arg85Ter Pathogenic/Likely pathogenic ★★ same type
- MAP1B p.Arg999Ter Pathogenic/Likely pathogenic ★★ same type
- MAP1B p.Ala966Val Uncertain significance ★★ ⚠ same type
- MAP1B p.Arg1399Cys Uncertain significance ★★ ⚠ same type
- MAP1B p.Arg1948Trp 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/map1b-p-ile171 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown