DNAJC19 c.-29G>T
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.305%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.1 | |
| Non-coding constraint | Z 1.05 | 1 kb window · o/e 0.93 · regional · uncalibrated |
| Overall | ||
| CADD | 6.619 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.305%
European (non-Finnish) · 3,558/1,166,122 alleles
Filtering AF
0.297%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.293%
Overall
0.241%
3,815/1,584,672 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.305% | 328 |
| South Asian | 0.129% | 773 |
| Remaining individualsnot grpmax-eligible | 0.117% | 853 |
| Finnishnot grpmax-eligible | 0.0607% | 1,648 |
| African / African-American | 0.0389% | 2,569 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0104% | 9,631 |
| Admixed American | 0.00716% | 13,974 |
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
- DNAJC19
- Coding
- c.-29G>T
- MANE Select
- NM_145261
- dbSNP
- rs181271620
- Type
- single nucleotide variant
- Location
- chr3:180989631 (GRCh38)
- Gene constraint
- LOEUF 1.547 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.50
Similar variants
- DNAJC19 c.130-1G>C Pathogenic ★★ same type
- DNAJC19 c.4-1G>A Likely pathogenic ★★ same type
- DNAJC19 c.55+1G>A Pathogenic/Likely pathogenic ★★ same type
- DNAJC19 p.Ala25Thr Uncertain significance ★★ ⚠ same type
- DNAJC19 p.Ala73Thr Uncertain significance ★★ same type
- DNAJC19 p.Arg20Cys Uncertain significance ★★ ⚠ same type
- DNAJC19 p.Arg84Gln Uncertain significance ★★ ⚠ same type
- DNAJC19 p.Gly68Asp 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/dnajc19-c-minus-29g-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown