SERPING1 p.Ser70=
c.210A>T · rs1484668063 · VCV2987637
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
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 -0.009 | GERP -3.6, phastCons 0.003 |
| Overall | ||
| CADD | 1.127 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,080 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000248%
4/1,614,140 alleles · very rare
exomes 4/1,461,884 · genomes 0/152,256 · joint denominator
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
- SERPING1
- Protein
- p.Ser70=
- Coding
- c.210A>T
- MANE Select
- NM_000062
- dbSNP
- rs1484668063
- Type
- single nucleotide variant
- Location
- chr11:57600037 (GRCh38)
- Gene constraint
- LOEUF 0.278 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.63 · 5 PDB
- Residue 70
- the 'disordered' region
Similar variants
- SERPING1 p.Ser70fs Pathogenic ★ same residue
- SERPING1 c.1030-1G>T Pathogenic ★★ same type
- SERPING1 c.51+1G>T Pathogenic ★★ same type
- SERPING1 c.51+3A>C Pathogenic/Likely pathogenic ★★ same type
- SERPING1 c.51+3A>G Pathogenic ★★ same type
- SERPING1 c.52-1G>A Pathogenic ★★ same type
- SERPING1 c.550+1G>A Pathogenic ★★ same type
- SERPING1 c.551-1G>C Pathogenic/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/serping1-p-ser70 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown