CALR p.Phe202=
c.606C>T · rs79497711 · VCV708616
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.895%, 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 0.21 | GERP -0.36, phastCons 0.14 |
| Overall | ||
| CADD | 11.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.895%
African / African-American · 672/75,042 alleles
Filtering AF
0.839%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.817%
Overall
0.0453%
732/1,614,170 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.895% | 112 |
| Remaining individualsnot grpmax-eligible | 0.0544% | 1,839 |
| Admixed American | 0.0283% | 3,530 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.000678% | 147,504 |
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
- CALR
- Protein
- p.Phe202=
- Coding
- c.606C>T
- MANE Select
- NM_004343
- dbSNP
- rs79497711
- Type
- single nucleotide variant
- Location
- chr19:12940356 (GRCh38)
- Gene constraint
- LOEUF 0.423 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.31 · 10 PDB
- Residue 202
- the '4 x approximate repeats' region; the 'disordered' region; the 'p-domain' region; a β-strand
Similar variants
- CALR c.193+41C>G Benign ★★ same type
- CALR c.194-41A>G Benign ★★ same type
- CALR c.817-9C>T Benign/Likely benign ★★ same type
- CALR c.960+128C>T Benign ★★ same type
- CALR c.960+290A>G Benign ★★ same type
- CALR c.961-239G>A Benign ★★ same type
- CALR c.-21T>C Benign ★★ same type
- CALR c.*54G>T Benign ★★ 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/calr-p-phe202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown