Is DNAH10 p.Arg3494= (c.10482G>A) pathogenic?

DNAH10 p.Arg3494= (c.10482G>A) is classified Benign in DNAH10 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-13). Low-frequency (popmax 3.19%, nfe); Associated with DNAH10-related disorder.

What condition is associated with DNAH10 p.Arg3494= (c.10482G>A)?

DNAH10 p.Arg3494= (c.10482G>A) is associated with DNAH10-related disorder (ClinVar).

How common is DNAH10 p.Arg3494= (c.10482G>A) in the general population?

DNAH10 p.Arg3494= (c.10482G>A) is low-frequency (popmax 3.19%, nfe) (gnomAD).

DNAH10 p.Arg3494=

c.10482G>A · rs11057392 · VCV3056135

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 3.19%, nfe)

Conditions

DNAH10-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.003	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.62	GERP -3
Overall
CADD	0.713	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.19% European (non-Finnish) · 37,651/1,179,892 alleles

Filtering AF 3.16% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.15%

Overall 2.67% 43,152/1,613,802 alleles · low-frequency

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	3.53%	28
European (non-Finnish)grpmax	3.19%	31
Amishnot grpmax-eligible	2.96%	34
Remaining individualsnot grpmax-eligible	2.15%	46
Admixed American	1.11%	90
South Asian	0.769%	130
Middle Eastern	0.544%	184
African / African-American	0.526%	190
Ashkenazi Jewishnot grpmax-eligible	0.253%	395
East Asian	0.00223%	44,876

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: DNAH10
Protein: p.Arg3494=
Coding: c.10482G>A
MANE Select: NM_001372106
dbSNP: rs11057392
Type: single nucleotide variant
Location: chr12:123914458 (GRCh38)
Gene constraint: LOEUF 0.763 · pLI <0.01 (gnomAD)
Residue 3494: the 'aaa 5' region

Full DNAH10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DNAH10-related disorder

Similar variants

DNAH10 p.Pro3309Ala Uncertain significance ★ ⚠ same condition
DNAH10 p.Gln999Glu Uncertain significance ⚠ same condition
DNAH10 p.Lys132Asn Uncertain significance ⚠ same condition
DNAH10 c.11766+6C>T Likely benign same condition
DNAH10 c.2987+8C>T Likely benign same condition
DNAH10 p.Ala1801= Benign same condition
DNAH10 p.Ala2444= Likely benign same condition
DNAH10 p.Arg3763= Likely benign 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/dnah10-p-arg3494 (accessed [today's date]).

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