Is DNAH10 p.Arg102Cys (c.304C>T) pathogenic?

DNAH10 p.Arg102Cys (c.304C>T) is classified Uncertain significance in DNAH10 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-08-09). AlphaMissense: likely benign (0.1083); Rare (popmax 0.173%, sas).

How common is DNAH10 p.Arg102Cys (c.304C>T) in the general population?

DNAH10 p.Arg102Cys (c.304C>T) is rare (popmax 0.173%, sas) (gnomAD).

What do computational predictors say about DNAH10 p.Arg102Cys (c.304C>T)?

AlphaMissense predicts likely benign (score 0.1083) — an in-silico prediction, not a clinical call.

DNAH10 p.Arg102Cys

c.304C>T · rs200881150 · VCV3049615

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1083 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.173%, sas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.1083	likely benign
REVEL	0.041	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.35	GERP 0.1, phastCons 0.003
Overall
CADD	14.05	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R41C vs ClinVar R102C) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.173% South Asian · 157/90,854 alleles

Filtering AF 0.151% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.142%

Overall 0.0468% 755/1,613,236 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.322%	311
South Asiangrpmax	0.173%	579
Remaining individualsnot grpmax-eligible	0.056%	1,785
Middle Eastern	0.033%	3,031
European (non-Finnish)	0.0295%	3,389
Admixed American	0.00834%	11,992
African / African-American	0.00267%	37,507

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.Arg102Cys
Coding: c.304C>T
MANE Select: NM_001372106
dbSNP: rs200881150
Type: single nucleotide variant
Location: chr12:123771606 (GRCh38)
Gene constraint: LOEUF 0.763 · pLI <0.01 (gnomAD)
Residue 102: the 'stem' region

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

Similar variants

DNAH10 p.Arg102His Likely benign ★ same residue
DNAH10 p.Ala2444Val Uncertain significance ★★ ⚠ same type
DNAH10 p.Arg2111Trp Uncertain significance ★★ ⚠ same type
DNAH10 p.Arg2957Gln Uncertain significance ★★ same type
DNAH10 p.Arg3955His Uncertain significance ★★ ⚠ same type
DNAH10 p.Asp3319Gly Uncertain significance ★★ ⚠ same type
DNAH10 p.Glu4042Gln Uncertain significance ★★ ⚠ same type
DNAH10 p.Gly4445Glu 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/dnah10-p-arg102cys (accessed [today's date]).

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