IGF2R p.Asp2152=
c.6456T>C · rs193107580 · VCV728388
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.261%, sas)
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 -2.8 | GERP -3.1 |
| Overall | ||
| CADD | 3.478 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.261%
South Asian · 236/90,390 alleles
Filtering AF
0.234%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.223%
Overall
0.0179%
288/1,606,074 alleles · rare
exomes 274/1,453,758 · genomes 14/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.261% | 383 |
| Middle Eastern | 0.0333% | 3,002 |
| Remaining individualsnot grpmax-eligible | 0.0322% | 3,109 |
| Admixed American | 0.0169% | 5,902 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0034% | 29,434 |
| European (non-Finnish) | 0.00162% | 61,831 |
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
- IGF2R
- Protein
- p.Asp2152=
- Coding
- c.6456T>C
- MANE Select
- NM_000876
- dbSNP
- rs193107580
- Type
- single nucleotide variant
- Location
- chr6:160089242 (GRCh38)
- Gene constraint
- LOEUF 0.421 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.48 · 24 PDB
- Residue 2152
- the mrh 15 domain
Similar variants
- IGF2R p.Asp2152His Uncertain significance ★ ⚠ same residue
- IGF2R p.Asp2219= Benign/Likely benign ★★ same type
- IGF2R p.Leu817Val Benign ★★ same type
- IGF2R p.Pro2129= Benign/Likely benign ★★ same type
- IGF2R p.His151Tyr Likely pathogenic ★ ⚠ same type
- IGF2R c.289+2T>C Uncertain significance ★ same type
- IGF2R p.Ala1033Pro Uncertain significance ★ ⚠ same type
- IGF2R p.Ala104Thr 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/igf2r-p-asp2152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown