Is CHD8 p.Arg1939= (c.5817C>T) pathogenic?

CHD8 p.Arg1939= (c.5817C>T) is classified Likely benign in CHD8 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-03-01). Ultra-rare (popmax 0.062%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CHD8 p.Arg1939= (c.5817C>T)?

CHD8 p.Arg1939= (c.5817C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CHD8 p.Arg1939= (c.5817C>T) in the general population?

CHD8 p.Arg1939= (c.5817C>T) is ultra-rare (popmax 0.062%, nfe) (gnomAD).

CHD8 p.Arg1939=

c.5817C>T · rs140310602 · VCV784679

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.062%, nfe)

Conditions

Inborn genetic diseases

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 1.4	GERP -2.7, phastCons 1
Overall
CADD	5.474	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.062% European (non-Finnish) · 732/1,179,882 alleles

Filtering AF 0.0583% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0568%

Overall 0.048% 775/1,613,950 alleles · ultra-rare exomes 733/1,461,682 · genomes 42/152,268 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.062%	1,612
Remaining individualsnot grpmax-eligible	0.048%	2,083
African / African-American	0.0107%	9,380
Finnishnot grpmax-eligible	0.00781%	12,798

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: CHD8
Protein: p.Arg1939=
Coding: c.5817C>T
MANE Select: NM_001170629
dbSNP: rs140310602
Type: single nucleotide variant
Location: chr14:21393978 (GRCh38)
Gene constraint: LOEUF 0.154 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 55.17 · 2 PDB
Residue 1939: the 'interaction with fam124b' region

Full CHD8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHD8 p.Arg1939Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
CHD8 p.Arg1939His Conflicting classifications of pathogenicity ★ ⚠ same residue
CHD8 c.3882+1G>A Pathogenic/Likely pathogenic ★★ same condition
CHD8 p.Arg1462Ter Pathogenic ★★ same condition
CHD8 p.Arg1582Ter Pathogenic/Likely pathogenic ★★ same condition
CHD8 p.Arg2217Ter Pathogenic ★★ same condition
CHD8 p.Arg243Ter Pathogenic ★★ same condition
CHD8 c.4921+4C>T Uncertain significance ★★ same condition

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/chd8-p-arg1939 (accessed [today's date]).

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