SLC19A2 c.807+81del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.27%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +81 | deep intronic (+81 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP 1.1, phastCons 0.007 |
| Non-coding constraint | Z 1.75 | 1 kb window · o/e 0.87 · regional · uncalibrated |
| Overall | ||
| CADD | 0.045 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.27%
African / African-American · 918/72,002 alleles
Filtering AF
1.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.18%
Overall
0.0707%
1,033/1,460,426 alleles · low-frequency
exomes 509/1,308,082 · genomes 524/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.27% | 78 |
| Middle Eastern | 0.164% | 608 |
| Admixed American | 0.0836% | 1,197 |
| Remaining individualsnot grpmax-eligible | 0.0786% | 1,272 |
| South Asian | 0.00229% | 43,637 |
| European (non-Finnish) | 0.00106% | 94,739 |
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
- SLC19A2
- Coding
- c.807+81del
- MANE Select
- NM_006996
- dbSNP
- rs564882105
- Type
- Deletion
- Location
- chr1:169477074 (GRCh38)
- Gene constraint
- LOEUF 0.852 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.99 · 2 PDB
Similar variants
- SLC19A2 p.Tyr144fs Pathogenic/Likely pathogenic ★★ same type
- SLC19A2 p.Ile354del Uncertain significance ★★ same type
- SLC19A2 c.1223+13del Likely benign ★★ same type
- SLC19A2 c.205-14del Benign/Likely benign ★★ same type
- SLC19A2 p.Asn333fs Pathogenic ★ same type
- SLC19A2 p.Glu451fs Pathogenic ★ same type
- SLC19A2 p.Leu304fs Likely pathogenic ★ same type
- SLC19A2 p.Met401fs Pathogenic ★ 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/slc19a2-c-807-plus-81del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown