IGF2 p.Thr30=
c.90C>T · rs74050127 · VCV714495
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.52%, afr)
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 |
|---|---|---|
| Pangolin | Δ0.23 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP -0.53, phastCons 0.85 |
| Overall | ||
| CADD | 15.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.52%
African / African-American · 1,887/75,006 alleles
Filtering AF
2.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.38%
Overall
0.129%
2,089/1,613,376 alleles · low-frequency
exomes 1,014/1,461,102 · genomes 1,075/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.52% | 40 |
| Remaining individualsnot grpmax-eligible | 0.158% | 631 |
| Admixed American | 0.125% | 800 |
| Middle Eastern | 0.066% | 1,516 |
| South Asian | 0.00769% | 13,012 |
| European (non-Finnish) | 0.00144% | 69,399 |
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
- IGF2
- Protein
- p.Thr30=
- Coding
- c.90C>T
- MANE Select
- NM_000612 · reported on NM_001127598
- dbSNP
- rs74050127
- Type
- single nucleotide variant
- Location
- chr11:2140207 (GRCh38)
- Gene constraint
- LOEUF 0.496 · pLI 0.96 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.95 · 16 PDB
- Residue 30
- a UniProt-annotated variant site (in srs3); the 'b' region
Similar variants
- IGF2 p.Glu30fs Pathogenic ★ same residue
- IGF2 c.157+5G>A Pathogenic ★★ same type
- IGF2 p.Glu36Ter Pathogenic/Likely pathogenic ★★ same type
- IGF2 p.Gly34Cys Likely pathogenic ★★ same type
- IGF2 p.Ser20Ter Likely pathogenic ★★ same type
- IGF2 p.Ala167Ser Uncertain significance ★★ ⚠ same type
- IGF2 p.Arg138Trp Uncertain significance ★★ ⚠ same type
- IGF2 p.Arg154Cys 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/igf2-p-thr30 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown