Is DNAJC19 c.209+95C>G pathogenic?

DNAJC19 c.209+95C>G is classified Likely benign in DNAJC19 (ClinVar, Single submitter, 2 submitters; last evaluated 2018-06-14). Rare (popmax 0.832%, nfe).

How common is DNAJC19 c.209+95C>G in the general population?

DNAJC19 c.209+95C>G is rare (popmax 0.832%, nfe) (gnomAD).

DNAJC19 c.209+95C>G

rs192120432 · VCV676722

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.832%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +95	deep intronic (+95 nt into the intron)
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.66	GERP -2.8
Non-coding constraint	Z 1.66	1 kb window · o/e 0.88 · regional · uncalibrated
Overall
CADD	0.077	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.832% European (non-Finnish) · 5,298/636,786 alleles

Filtering AF 0.813% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.806%

Overall 0.671% 6,798/1,013,416 alleles · rare exomes 5,907/861,182 · genomes 891/152,234 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	1.35%	74
European (non-Finnish)grpmax	0.832%	120
Amishnot grpmax-eligible	0.768%	130
Remaining individualsnot grpmax-eligible	0.549%	182
Ashkenazi Jewishnot grpmax-eligible	0.48%	208
Admixed American	0.249%	402
African / African-American	0.113%	889
South Asian	0.0824%	1,214
Middle Eastern	0.0308%	3,246

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.209+95C>G
MANE Select: NM_145261
dbSNP: rs192120432
Type: single nucleotide variant
Location: chr3:180986848 (GRCh38)
Gene constraint: LOEUF 1.547 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.50

Full DNAJC19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-209-plus-95c-g (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown