ALMS1 p.Ser3094=
c.9282A>G · VCV3910196
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 3.6 | GERP 0.67, phastCons 1 |
| Overall | ||
| CADD | 6.821 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ALMS1
- Protein
- p.Ser3094=
- Coding
- c.9282A>G
- MANE Select
- NM_001378454
- Type
- single nucleotide variant
- Location
- chr2:73491241 (GRCh38)
- Gene constraint
- LOEUF 0.825 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Similar variants
- ALMS1 p.Ser3094Leu Uncertain significance ★★ ⚠ same residue
- ALMS1 c.10079-1G>C Likely pathogenic ★★ same type
- ALMS1 c.10214-2A>G Likely pathogenic ★★ same type
- ALMS1 c.10384+1G>A Likely pathogenic ★★ same type
- ALMS1 c.10385-2A>G Pathogenic ★★ same type
- ALMS1 c.11547+3A>T Likely pathogenic ★★ same type
- ALMS1 c.11668+1G>T Pathogenic/Likely pathogenic ★★ same type
- ALMS1 c.11669-1G>A 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/alms1-p-ser3094 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown