SAG p.Val48=
c.144C>T · rs534970020 · VCV1125342
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0401%, eas)
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 -5.6 | GERP -3.8 |
| Overall | ||
| CADD | 1.451 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0401%
East Asian · 18/44,876 alleles
Filtering AF
0.0259%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0214%
Overall
0.00297%
48/1,613,728 alleles · ultra-rare
exomes 38/1,461,472 · genomes 10/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0401% | 2,493 |
| African / African-American | 0.0133% | 7,503 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
| European (non-Finnish) | 0.00144% | 69,392 |
| South Asian | 0.0011% | 91,078 |
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
- SAG
- Protein
- p.Val48=
- Coding
- c.144C>T
- MANE Select
- NM_000541
- dbSNP
- rs534970020
- Type
- single nucleotide variant
- Location
- chr2:233318758 (GRCh38)
- Structure
- AlphaFold pLDDT 83.02 · 7 PDB
Similar variants
- SAG c.1023-2A>G Likely pathogenic ★★ same type
- SAG c.1103-2A>C Pathogenic/Likely pathogenic ★★ same type
- SAG c.136+2T>C Likely pathogenic ★★ same type
- SAG c.136+2T>G Pathogenic/Likely pathogenic ★★ same type
- SAG c.181+1G>A Likely pathogenic ★★ same type
- SAG c.182-2A>G Pathogenic/Likely pathogenic ★★ same type
- SAG c.376-2A>G Pathogenic/Likely pathogenic ★★ same type
- SAG c.435+1G>A Likely pathogenic ★★ 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/sag-p-val48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown