PRCD c.74+14C>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00545%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +14 | near-intronic (+14 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not looked up on this page · why |
| Constraint at this position | ||
| Conservation | phyloP -2.3 | GERP -3.1 |
| Non-coding constraint | Z 5.01 | 1 kb window · o/e 0.63 · regional · uncalibrated |
| Overall | ||
| CADD | 1.039 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00545%
East Asian · 1/18,336 alleles
Filtering AF
0.00015%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.2e-05%
Overall
0.000866%
6/692,976 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00545% | 18,336 |
| Remaining individualsnot grpmax-eligible | 0.00353% | 28,294 |
| Finnishnot grpmax-eligible | 0.00309% | 32,404 |
| European (non-Finnish) | 0.000563% | 177,485 |
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
- PRCD
- Coding
- c.74+14C>A
- MANE Select
- NM_134268 · reported on NM_001077620
- dbSNP
- rs200645008
- Type
- single nucleotide variant
- Location
- chr17:76540229 (GRCh38)
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/prcd-c-74-plus-14c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown