CD44 c.367+7T>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.07%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.17 | GERP -2.2, phastCons 0.22 |
| Non-coding constraint | Z 0.77 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 10.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.07%
African / African-American · 1,554/74,990 alleles
Filtering AF
1.99%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.95%
Overall
0.108%
1,737/1,614,004 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.07% | 48 |
| Remaining individualsnot grpmax-eligible | 0.147% | 679 |
| Admixed American | 0.107% | 938 |
| Middle Eastern | 0.066% | 1,516 |
| South Asian | 0.00769% | 13,011 |
| European (non-Finnish) | 0.00136% | 73,746 |
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
- CD44
- Coding
- c.367+7T>C
- MANE Select
- NM_000610
- dbSNP
- rs116243547
- Type
- single nucleotide variant
- Location
- chr11:35180414 (GRCh38)
- Gene constraint
- LOEUF 0.654 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.31 · 7 PDB
Similar variants
- CD44 p.Arg463Gln Benign ★★ same type
- CD44 p.Arg673Gln Likely benign ★★ ⚠ same type
- CD44 p.Gly462= Benign ★★ same type
- CD44 p.Ile457Val Benign ★★ same type
- CD44 p.Phe245= Benign ★★ same type
- CD44 p.Thr163= Benign ★★ same type
- CD44 p.Thr393Met Benign ★★ ⚠ same type
- CD44 p.Thr415= 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/cd44-c-367-plus-7t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown