SON p.Ala897=
c.2691G>A · rs61746013 · VCV790892
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 7.36%, mid) — too common for a highly-penetrant pathogenic allele
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 -2.6 | GERP -6.4 |
| Overall | ||
| CADD | 1.249 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.36%
Middle Eastern · 446/6,058 alleles
Filtering AF
6.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.58%
Overall
0.586%
9,459/1,614,084 alleles · common
exomes 8,567/1,461,862 · genomes 892/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 7.36% | 14 |
| Ashkenazi Jewishnot grpmax-eligible | 1.92% | 52 |
| Remaining individualsnot grpmax-eligible | 0.859% | 116 |
| Admixed American | 0.858% | 117 |
| European (non-Finnish) | 0.569% | 176 |
| South Asian | 0.469% | 213 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| African / African-American | 0.197% | 507 |
| Finnishnot grpmax-eligible | 0.156% | 640 |
| East Asian | 0.0111% | 8,977 |
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
- SON
- Protein
- p.Ala897=
- Coding
- c.2691G>A
- MANE Select
- NM_138927
- dbSNP
- rs61746013
- Type
- single nucleotide variant
- Location
- chr21:33551922 (GRCh38)
- Gene constraint
- LOEUF 0.051 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.48 · 4 PDB
Similar variants
- SON p.Ala897Val Uncertain significance ★ ⚠ same residue
- SON c.6321+1G>A Pathogenic ★★ same type
- SON p.Arg1081Ter Pathogenic ★★ same type
- SON p.Arg1112Ter Pathogenic ★★ same type
- SON p.Arg1825Ter Pathogenic ★★ same type
- SON p.Arg2008Ter Pathogenic ★★ same type
- SON p.Gln96Ter Pathogenic/Likely pathogenic ★★ same type
- SON c.6657+160A>C Uncertain significance ★★ 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/son-p-ala897 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown