TP53 c.993+232G>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.56e-05%, nfe)
Conditions
1
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +232 | deep intronic (+232 nt into the intron) |
|---|---|---|
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.29 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -0.17 | GERP -1.9, phastCons 0.002 |
| Overall | ||
| CADD | 7.264 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.56e-05%
European (non-Finnish) · 1/1,168,230 alleles
Overall
6.28e-05%
1/1,593,294 alleles · very rare
exomes 1/1,441,136 · genomes 0/152,158 · joint denominator
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
- TP53
- Coding
- c.993+232G>C
- MANE Select
- NM_000546
- dbSNP
- rs1470589675
- Type
- single nucleotide variant
- Location
- chr17:7673303 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.83 · 321 PDB
Similar variants
- TP53 c.375+5G>A Likely pathogenic ★★★ same condition
- TP53 c.919+1G>A Pathogenic ★★★ same condition
- TP53 c.97-1G>A Pathogenic ★★★ same condition
- TP53 p.Ala138Pro Likely pathogenic ★★★ same condition
- TP53 p.Ala138Val Likely pathogenic ★★★ same condition
- TP53 p.Ala347Asp Pathogenic ★★★ same condition
- TP53 p.Arg110Gly Likely pathogenic ★★★ ⚠ same condition
- TP53 p.Arg110Leu Pathogenic ★★★ ⚠ same condition
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/tp53-c-993-plus-232g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown