CD164 c.331+58G>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.67%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +58 | deep intronic (+58 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.29 | GERP -1.1 |
| Non-coding constraint | Z -1.98 | 1 kb window · o/e 1.15 · regional · uncalibrated |
| Overall | ||
| CADD | 4.886 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.67%
African / African-American · 1,123/67,436 alleles
Filtering AF
1.58%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.55%
Overall
0.102%
1,261/1,231,910 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.67% | 60 |
| Remaining individualsnot grpmax-eligible | 0.106% | 941 |
| Admixed American | 0.103% | 971 |
| Middle Eastern | 0.0744% | 1,343 |
| South Asian | 0.00962% | 10,392 |
| European (non-Finnish) | 0.00144% | 69,373 |
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
- CD164
- Coding
- c.331+58G>C
- MANE Select
- NM_006016
- dbSNP
- rs114995468
- Type
- single nucleotide variant
- Location
- chr6:109377842 (GRCh38)
- Gene constraint
- LOEUF 1.232 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 67.15
Similar variants
- CD164 p.Arg192Ter Uncertain significance ★★ same type
- CD164 p.Asn121Ser Uncertain significance ★★ ⚠ same type
- CD164 p.Asn32Lys Uncertain significance ★★ ⚠ same type
- CD164 p.Asp107Asn Uncertain significance ★★ ⚠ same type
- CD164 p.Leu15Val Uncertain significance ★★ ⚠ same type
- CD164 p.Leu183Pro Uncertain significance ★★ ⚠ same type
- CD164 p.Leu9Phe Uncertain significance ★★ ⚠ same type
- CD164 p.Lys137Gln Uncertain significance ★★ ⚠ 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/cd164-c-331-plus-58g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown