ST7 p.Ser180=
c.540G>A · rs77060569 · VCV724738
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.108%, 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 -10 | GERP -5 |
| Overall | ||
| CADD | 2.281 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.108%
East Asian · 48/44,608 alleles
Filtering AF
0.0834%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0748%
Overall
0.00497%
80/1,610,252 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.108% | 929 |
| African / African-American | 0.00938% | 10,661 |
| Remaining individualsnot grpmax-eligible | 0.00482% | 20,765 |
| Finnishnot grpmax-eligible | 0.00313% | 31,951 |
| South Asian | 0.0022% | 45,448 |
| European (non-Finnish) | 0.00153% | 65,437 |
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
- ST7
- Protein
- p.Ser180=
- Coding
- c.540G>A
- MANE Select
- NM_001369598
- dbSNP
- rs77060569
- Type
- single nucleotide variant
- Location
- chr7:117130581 (GRCh38)
- Gene constraint
- LOEUF 0.52 · pLI 0.92 (gnomAD)
- Structure
- AlphaFold pLDDT 80.60
Similar variants
- ST7 c.1638+860G>T Likely benign ★★ same type
- ST7 c.1638+917G>T Likely benign ★★ same type
- ST7 c.1638+799A>T Uncertain significance ★ ⚠ same type
- ST7 c.1638+818C>T Uncertain significance ★ ⚠ same type
- ST7 c.1638+859C>T Uncertain significance ★ ⚠ same type
- ST7 c.1638+880A>G Uncertain significance ★ ⚠ same type
- ST7 c.1638+887C>T Uncertain significance ★ ⚠ same type
- ST7 p.Ala188Gly 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/st7-p-ser180 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown