SYNCRIP c.375+19C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00225%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +19 | near-intronic (+19 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.49 | GERP -0.39 |
| Non-coding constraint | Z -3.50 | 1 kb window · o/e 1.27 · regional · uncalibrated |
| Overall | ||
| CADD | 1.855 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00225%
East Asian · 1/44,358 alleles
Filtering AF
0.000195%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000128%
Overall
0.000458%
7/1,529,170 alleles · very rare
exomes 6/1,377,096 · genomes 1/152,074 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00225% | 44,358 |
| European (non-Finnish) | 0.000542% | 184,345 |
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
- SYNCRIP
- Coding
- c.375+19C>T
- MANE Select
- NM_006372
- Type
- single nucleotide variant
- Location
- chr6:85640202 (GRCh38)
- Gene constraint
- LOEUF 0.249 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 70.83 · 4 PDB
Similar variants
- SYNCRIP p.Ala216Thr Uncertain significance ★★ same type
- SYNCRIP p.Asn243Ser Uncertain significance ★★ ⚠ same type
- SYNCRIP p.Pro440Leu Uncertain significance ★★ ⚠ same type
- SYNCRIP p.Pro508Leu Uncertain significance ★★ ⚠ same type
- SYNCRIP p.Ser116Gly Uncertain significance ★★ ⚠ same type
- SYNCRIP p.Glu612Val Likely benign ★★ ⚠ same type
- SYNCRIP p.Arg446Ter Pathogenic ★ same type
- SYNCRIP c.803-3C>A 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/syncrip-c-375-plus-19c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown