ARVCF p.Ser567=
c.1701G>A · VCV3905241
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0551%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.3 | GERP -3.4 |
| Overall | ||
| CADD | 2.786 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0551%
Admixed American · 26/47,148 alleles
Filtering AF
0.0386%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0331%
Overall
0.0149%
227/1,524,050 alleles · ultra-rare
exomes 196/1,371,730 · genomes 31/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0551% | 1,813 |
| East Asian | 0.0305% | 3,274 |
| European (non-Finnish) | 0.0159% | 6,304 |
| Remaining individualsnot grpmax-eligible | 0.00857% | 11,667 |
| Ashkenazi Jewishnot grpmax-eligible | 0.004% | 25,014 |
| African / African-American | 0.00277% | 36,071 |
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.Ser567=
- Coding
- c.1701G>A
- MANE Select
- NM_001670
- Type
- single nucleotide variant
- Location
- chr22:19977584 (GRCh38)
- Gene constraint
- LOEUF 1.032 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.73
Similar variants
- 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
- ARVCF c.1871-172A>C 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-ser567 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown