IMMT p.Ser157=
c.471G>T · rs186479748 · VCV728851
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.476%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.014 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.54 | acceptor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP -6.4 | GERP -4.2 |
| Overall | ||
| CADD | 11.26 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.476%
African / African-American · 357/74,934 alleles
Filtering AF
0.436%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.42%
Overall
0.0258%
415/1,610,488 alleles · rare
exomes 184/1,458,266 · genomes 231/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.476% | 210 |
| Admixed American | 0.047% | 2,128 |
| Remaining individualsnot grpmax-eligible | 0.0369% | 2,712 |
| Middle Eastern | 0.0165% | 6,058 |
| South Asian | 0.00111% | 90,390 |
| European (non-Finnish) | 0.000424% | 235,613 |
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
- IMMT
- Protein
- p.Ser157=
- Coding
- c.471G>T
- MANE Select
- NM_006839
- dbSNP
- rs186479748
- Type
- single nucleotide variant
- Location
- chr2:86171296 (GRCh38)
- Gene constraint
- LOEUF 0.668 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.81 · 1 PDB
Similar variants
- IMMT p.Ser157Leu Uncertain significance ★ ⚠ same residue
- IMMT c.119+4T>C Benign ★★ same type
- IMMT p.Glu435Lys Likely benign ★★ same type
- IMMT p.Thr171= Benign ★★ same type
- IMMT p.Ala227Gly Uncertain significance ★ ⚠ same type
- IMMT p.Ala259Thr Uncertain significance ★ same type
- IMMT p.Ala347Thr Uncertain significance ★ ⚠ same type
- IMMT p.Ala444Val 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/immt-p-ser157 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown