Is PRCD c.74+8A>T pathogenic?

PRCD c.74+8A>T is classified Likely benign in PRCD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-12-30). Ultra-rare (popmax 0.0867%, sas).

How common is PRCD c.74+8A>T in the general population?

PRCD c.74+8A>T is ultra-rare (popmax 0.0867%, sas) (gnomAD).

PRCD c.74+8A>T

rs548816444 · VCV2986744

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0867%, sas)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +8	near-intronic (+8 nt from the splice site)
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.087	GERP -2
Non-coding constraint	Z 5.01	1 kb window · o/e 0.63 · regional · uncalibrated
Overall
CADD	6.922	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0867% South Asian · 72/83,078 alleles

Filtering AF 0.0705% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0647%

Overall 0.00588% 78/1,326,476 alleles · ultra-rare exomes 76/1,198,866 · genomes 2/127,610 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0867%	1,154
Middle Eastern	0.0402%	2,486
Remaining individualsnot grpmax-eligible	0.00622%	16,066
European (non-Finnish)	0.000102%	984,252

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+8A>T
MANE Select: NM_001077620
dbSNP: rs548816444
Type: single nucleotide variant
Location: chr17:76540223 (GRCh38)

Full PRCD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-8a-t (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown