ALMS1 p.Arg3702=
c.11104C>A · rs747747269 · VCV1004077
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00834%, amr)
Conditions
2
Cardiovascular phenotype
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 0.15 | GERP -2.6 |
| Overall | ||
| CADD | 0.273 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00834%
Admixed American · 5/59,964 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.000682%
11/1,613,942 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00834% | 11,993 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| European (non-Finnish) | 0.000424% | 235,998 |
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
- ALMS1
- Protein
- p.Arg3702=
- Coding
- c.11104C>A
- MANE Select
- NM_001378454
- dbSNP
- rs747747269
- Type
- single nucleotide variant
- Location
- chr2:73572981 (GRCh38)
- Gene constraint
- LOEUF 0.825 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 3702
- the 'disordered' region
Similar variants
- ALMS1 p.Arg3702Ter Pathogenic ★★ same residue
- ALMS1 p.Arg3702Gln Uncertain significance ★★ ⚠ same residue
- ALMS1 p.Arg3702Leu Uncertain significance ★ ⚠ same residue
- ALMS1 c.10079-1G>C Likely pathogenic ★★ same condition
- ALMS1 c.10214-2A>G Likely pathogenic ★★ same condition
- ALMS1 c.10384+1G>A Likely pathogenic ★★ same condition
- ALMS1 c.10385-2A>G Pathogenic ★★ same condition
- ALMS1 c.11547+3A>T Likely pathogenic ★★ same condition
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-arg3702 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown