LAMB1 p.Phe1092=
c.3276C>T · rs946517228 · VCV2191894
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00401%, afr)
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 -4.4 | GERP -5.8 |
| Overall | ||
| CADD | 0.673 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
African / African-American · 3/74,878 alleles
Filtering AF
0.00165%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00142%
Overall
0.00211%
34/1,611,726 alleles · very rare
exomes 29/1,459,492 · genomes 5/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00401% | 24,959 |
| European (non-Finnish) | 0.00238% | 42,090 |
| East Asian | 0.00223% | 44,846 |
| Finnishnot grpmax-eligible | 0.00156% | 63,984 |
| South Asian | 0.0011% | 90,962 |
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
- LAMB1
- Protein
- p.Phe1092=
- Coding
- c.3276C>T
- MANE Select
- NM_002291
- dbSNP
- rs946517228
- Type
- single nucleotide variant
- Location
- chr7:107952027 (GRCh38)
- Gene constraint
- LOEUF 0.601 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.99 · 3 PDB
- Residue 1092
- the laminin egf-like 12 domain
Similar variants
- LAMB1 c.4188+1G>C Pathogenic/Likely pathogenic ★★ same type
- LAMB1 p.Arg397Ter Pathogenic ★★ same type
- LAMB1 p.Gln577Ter Pathogenic ★★ same type
- LAMB1 c.1985+5G>T Uncertain significance ★★ same type
- LAMB1 c.4746-3C>A Uncertain significance ★★ same type
- LAMB1 p.Ala1069Val Uncertain significance ★★ ⚠ same type
- LAMB1 p.Ala1239Thr Uncertain significance ★★ ⚠ same type
- LAMB1 p.Ala1331Gly 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/lamb1-p-phe1092 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown