TP53 c.74+57del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 +57 | deep intronic (+57 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -0.94 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,052 alleles
Overall
6.2e-05%
1/1,613,362 alleles · very rare
exomes 1/1,461,324 · genomes 0/152,038 · 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.74+57del
- MANE Select
- NM_000546
- dbSNP
- rs1555526956
- Type
- Deletion
- Location
- chr17:7676464 (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.993+1del Likely pathogenic ★★★ same condition
- TP53 p.Arg213fs Pathogenic ★★★ same condition
- TP53 p.Leu252_Ile254del Pathogenic ★★★ same condition
- TP53 p.Lys382fs Likely pathogenic ★★★ same condition
- TP53 c.283_375+21del Likely pathogenic ★★ same condition
- TP53 c.560-19_560-9del Pathogenic/Likely pathogenic ★★ same condition
- TP53 c.917_919+10del Pathogenic/Likely pathogenic ★★ same condition
- TP53 c.920-2del Likely 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-74-plus-57del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown