ARVCF p.Pro661=
c.1983C>T · rs78866590 · VCV737350
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.37%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7 | GERP -3.7 |
| Overall | ||
| CADD | 0.955 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.37%
East Asian · 616/44,836 alleles
Filtering AF
1.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.25%
Overall
0.0411%
662/1,611,536 alleles · low-frequency
exomes 601/1,459,316 · genomes 61/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.37% | 73 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,468 |
| South Asian | 0.011% | 9,098 |
| Admixed American | 0.00501% | 19,971 |
| European (non-Finnish) | 0.00127% | 78,608 |
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
- ARVCF
- Protein
- p.Pro661=
- Coding
- c.1983C>T
- MANE Select
- NM_001670
- dbSNP
- rs78866590
- Type
- single nucleotide variant
- Location
- chr22:19974217 (GRCh38)
- Gene constraint
- LOEUF 1.032 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.73
Similar variants
- ARVCF p.Pro661Arg Uncertain significance ★ ⚠ same residue
- ARVCF p.Gly172Ser Uncertain significance ★★ ⚠ same type
- ARVCF p.Val958Ile Uncertain significance ★★ ⚠ same type
- ARVCF c.1396+18A>G Benign ★★ same type
- ARVCF c.1396+198C>T Benign ★★ same type
- ARVCF c.1396+40G>A Benign ★★ same type
- ARVCF c.1397-146G>A Benign ★★ same type
- ARVCF c.1397-7C>T 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/arvcf-p-pro661 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown