MET p.Asn856=
c.2568T>C · rs118057172 · VCV220030
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0546%, afr)
Conditions
2
renal cell carcinoma
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 2.4 | GERP 0.56, phastCons 1 |
| Overall | ||
| CADD | 6.667 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0546%
African / African-American · 41/75,026 alleles
Filtering AF
0.0413%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0367%
Overall
0.00353%
57/1,613,748 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0546% | 1,830 |
| East Asian | 0.00892% | 11,214 |
| Admixed American | 0.005% | 19,991 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,826 |
| South Asian | 0.0022% | 45,535 |
| European (non-Finnish) | 0.000339% | 294,944 |
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
- MET
- Protein
- p.Asn856=
- Coding
- c.2568T>C
- MANE Select
- NM_024755 · reported on NM_000245
- dbSNP
- rs118057172
- Type
- single nucleotide variant
- Location
- chr7:116763253 (GRCh38)
- Structure
- AlphaFold pLDDT 52.38
- Residue 856
- the 'disordered' region
Similar variants
- MET p.Asn856Lys Uncertain significance ★ ⚠ same residue
- MET p.Asn856Tyr Uncertain significance ★ ⚠ same residue
- MET p.His1094Arg Pathogenic/Likely pathogenic ★★ ⚠ same condition
- MET p.Met1131Thr Pathogenic/Likely pathogenic ★★ same condition
- MET p.Val1092Ile Pathogenic/Likely pathogenic ★★ same condition
- MET p.Val1220Ile Pathogenic/Likely pathogenic ★★ ⚠ same condition
- MET c.1200+2T>C Uncertain significance ★★ same condition
- MET c.1392+1G>T Uncertain significance ★★ 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/met-p-asn856 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown