HAL p.Ala526=
c.1578A>G · rs201071054 · VCV3035284
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00653%, nfe)
Conditions
1
HAL-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.107 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -3.4 |
| Overall | ||
| CADD | 1.262 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00653%
European (non-Finnish) · 77/1,178,614 alleles
Filtering AF
0.0053%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0049%
Overall
0.00496%
80/1,612,550 alleles · very rare
exomes 78/1,460,348 · genomes 2/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00653% | 15,307 |
| Finnishnot grpmax-eligible | 0.00468% | 21,346 |
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
- HAL
- Protein
- p.Ala526=
- Coding
- c.1578A>G
- MANE Select
- NM_002108
- dbSNP
- rs201071054
- Type
- single nucleotide variant
- Location
- chr12:95978020 (GRCh38)
- Gene constraint
- LOEUF 1.213 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.83
Disease context
HAL-related disorder
Similar variants
- HAL c.248-5T>C Likely benign same condition
- HAL p.Ile600= Likely benign same condition
- HAL p.Pro652= Likely benign same condition
- HAL p.Pro95= Likely benign same condition
- HAL c.*392C>T Uncertain significance ★★ same type
- HAL p.Arg9Cys Uncertain significance ★★ ⚠ same type
- HAL p.Asn476Lys Uncertain significance ★★ ⚠ same type
- HAL p.Glu472Lys 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/hal-p-ala526 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown