CRYM c.795+72T>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 64.3%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +72 | deep intronic (+72 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.23 | GERP -4.2 |
| Non-coding constraint | Z 1.50 | 1 kb window · o/e 0.88 · regional · uncalibrated |
| Overall | ||
| CADD | 6.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
64.3%
African / African-American · 47,997/74,656 alleles
Filtering AF
63.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 63.6%
Overall
26.4%
422,363/1,601,130 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 64.3% | 2 |
| Amishnot grpmax-eligible | 34.5% | 3 |
| Finnishnot grpmax-eligible | 29.1% | 3 |
| South Asian | 25.7% | 4 |
| Remaining individualsnot grpmax-eligible | 25.6% | 4 |
| European (non-Finnish) | 25.3% | 4 |
| Middle Eastern | 25.2% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 22% | 5 |
| Admixed American | 20.7% | 5 |
| East Asian | 0.235% | 426 |
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
- CRYM
- Coding
- c.795+72T>C
- MANE Select
- NM_001376256
- dbSNP
- rs226048
- Type
- single nucleotide variant
- Location
- chr16:21261965 (GRCh38)
- Gene constraint
- LOEUF 0.841 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.06 · 1 PDB
Similar variants
- CRYM p.Ala178Glu Uncertain significance ★★ ⚠ same type
- CRYM p.Glu172Gly Uncertain significance ★★ ⚠ same type
- CRYM p.Leu72Val Uncertain significance ★★ ⚠ same type
- CRYM p.Met295Ile Uncertain significance ★★ ⚠ same type
- CRYM p.Thr95Ser Uncertain significance ★★ ⚠ same type
- CRYM p.Val4Leu Uncertain significance ★★ ⚠ same type
- CRYM c.171-118C>T Benign ★★ same type
- CRYM c.171-19G>A Likely 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/crym-c-795-plus-72t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown