ALMS1 p.Ile1998=
c.5994T>A · rs774242715 · VCV1089711
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00333%, 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 1.3 | GERP -0.65, phastCons 0.98 |
| Overall | ||
| CADD | 1.481 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,002 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000137%
2/1,461,784 alleles · very rare
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.Ile1998=
- Coding
- c.5994T>A
- MANE Select
- NM_001378454
- dbSNP
- rs774242715
- Type
- single nucleotide variant
- Location
- chr2:73452521 (GRCh38)
- Gene constraint
- LOEUF 0.825 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 1998
- the '34 x 47 aa approximate tandem repeat' region
Similar variants
- 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
- ALMS1 c.11668+1G>T Pathogenic/Likely pathogenic ★★ same condition
- ALMS1 c.11669-1G>A Pathogenic ★★ same condition
- ALMS1 c.11669-1G>C Pathogenic/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-ile1998 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown