CROCC p.Asp649=
c.1947C>T · rs751980652 · VCV2638374
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.101%, mid)
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 -1.5 | GERP -3.4 |
| Overall | ||
| CADD | 8.905 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.101%
Middle Eastern · 6/5,912 alleles
Filtering AF
0.0441%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0301%
Overall
0.0065%
101/1,554,012 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.101% | 985 |
| Remaining individualsnot grpmax-eligible | 0.0216% | 4,632 |
| Admixed American | 0.0215% | 4,659 |
| African / African-American | 0.0109% | 9,180 |
| European (non-Finnish) | 0.0054% | 18,533 |
| East Asian | 0.00241% | 41,522 |
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
- CROCC
- Protein
- p.Asp649=
- Coding
- c.1947C>T
- MANE Select
- NM_014675
- dbSNP
- rs751980652
- Type
- single nucleotide variant
- Location
- chr1:16944238 (GRCh38)
- Gene constraint
- LOEUF 1.165 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.58 · 2 PDB
Similar variants
- CROCC p.Asp649Glu Uncertain significance ★ ⚠ same residue
- CROCC p.Arg1094Trp Uncertain significance ★★ ⚠ same type
- CROCC p.Asp1119His Uncertain significance ★★ ⚠ same type
- CROCC p.Gly486Arg Uncertain significance ★★ ⚠ same type
- CROCC p.Arg1729Gln Likely benign ★★ same type
- CROCC p.Arg1908Cys Benign ★★ ⚠ same type
- CROCC p.Arg675His Benign ★★ same type
- CROCC p.Arg691His 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/crocc-p-asp649 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown