PDCD1 c.627+252C>T
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 21.8%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +252 | deep intronic (+252 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -0.46 |
| Overall | ||
| CADD | 1.292 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
21.8%
East Asian · 1,110/5,092 alleles
Filtering AF
20.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 20.3%
Overall
10.3%
15,347/149,066 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 21.8% | 5 |
| Middle Eastern | 16% | 6 |
| Admixed American | 15% | 7 |
| South Asian | 12.6% | 8 |
| Remaining individualsnot grpmax-eligible | 11.8% | 8 |
| African / African-American | 11.2% | 9 |
| Ashkenazi Jewishnot grpmax-eligible | 10.3% | 10 |
| Amishnot grpmax-eligible | 10.2% | 10 |
| European (non-Finnish) | 8.31% | 12 |
| Finnishnot grpmax-eligible | 5.72% | 17 |
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
- PDCD1
- Coding
- c.627+252C>T
- MANE Select
- NM_005018
- dbSNP
- rs41386349
- Type
- single nucleotide variant
- Location
- chr2:241851697 (GRCh38)
- Gene constraint
- LOEUF 0.891 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 74.53 · 38 PDB
Similar variants
- PDCD1 c.437-115G>A Benign ★★ same type
- PDCD1 c.593-56C>G Benign ★★ same type
- PDCD1 c.627+189G>A Benign ★★ same type
- PDCD1 c.628-110A>G Benign ★★ same type
- PDCD1 c.76+126G>C Benign ★★ same type
- PDCD1 c.76+15C>T Benign ★★ same type
- PDCD1 c.*889G>A Benign ★★ same type
- PDCD1 p.Ala215Val Benign ★★ 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/pdcd1-c-627-plus-252c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown