LAMA5 p.Ala1908=
c.5724C>T · rs142712051 · VCV2069560
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.245%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.68 | GERP -2 |
| Overall | ||
| CADD | 1.058 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.245%
African / African-American · 174/71,162 alleles
Filtering AF
0.215%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.203%
Overall
0.0127%
195/1,534,904 alleles · rare
exomes 84/1,384,048 · genomes 111/150,856 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.245% | 409 |
| Remaining individualsnot grpmax-eligible | 0.017% | 5,896 |
| Admixed American | 0.00925% | 10,808 |
| European (non-Finnish) | 0.000611% | 163,594 |
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
- LAMA5
- Protein
- p.Ala1908=
- Coding
- c.5724C>T
- MANE Select
- NM_005560
- dbSNP
- rs142712051
- Type
- single nucleotide variant
- Location
- chr20:62324124 (GRCh38)
- Gene constraint
- LOEUF 0.779 · pLI <0.01 (gnomAD)
- Residue 1908
- a UniProt-annotated variant site (in); the laminin egf-like 17 domain
Similar variants
- LAMA5 p.Ala1908Thr Benign ★★ same residue
- LAMA5 c.4652+3G>A Uncertain significance ★★ same type
- LAMA5 p.Ala1020Val Uncertain significance ★★ same type
- LAMA5 p.Ala1212Val Uncertain significance ★★ ⚠ same type
- LAMA5 p.Ala1582Val Uncertain significance ★★ same type
- LAMA5 p.Ala1835Thr Uncertain significance ★★ same type
- LAMA5 p.Ala2076Ser Uncertain significance ★★ ⚠ same type
- LAMA5 p.Ala2261Val 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/lama5-p-ala1908 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown