Is DNAH7 p.Arg3772Thr (c.11315G>C) pathogenic?

DNAH7 p.Arg3772Thr (c.11315G>C) is classified Uncertain significance in DNAH7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-13). AlphaMissense: likely benign (0.173); Ultra-rare (popmax 0.0368%, nfe).

How common is DNAH7 p.Arg3772Thr (c.11315G>C) in the general population?

DNAH7 p.Arg3772Thr (c.11315G>C) is ultra-rare (popmax 0.0368%, nfe) (gnomAD).

What do computational predictors say about DNAH7 p.Arg3772Thr (c.11315G>C)?

AlphaMissense predicts likely benign (score 0.173) — an in-silico prediction, not a clinical call.

DNAH7 p.Arg3772Thr

c.11315G>C · rs373836682 · VCV2342417

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.173 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0368%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.173	likely benign
REVEL	0.147	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 4	GERP 1.4, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 331 kb · p 0.14 · regional, not allelic
Overall
CADD	23.4	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.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0368% European (non-Finnish) · 434/1,180,032 alleles

Filtering AF 0.0339% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0327%

Overall 0.0279% 450/1,614,002 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0368%	2,719
Remaining individualsnot grpmax-eligible	0.0128%	7,810
Admixed American	0.00667%	14,999
Finnishnot grpmax-eligible	0.00312%	32,013
African / African-American	0.00267%	37,448

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: DNAH7
Protein: p.Arg3772Thr
Coding: c.11315G>C
MANE Select: NM_018897
dbSNP: rs373836682
Type: single nucleotide variant
Location: chr2:195771778 (GRCh38)
Gene constraint: LOEUF 0.961 · pLI <0.01 (gnomAD)

Full DNAH7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAH7 p.Arg1884Gln Uncertain significance ★★ ⚠ same type
DNAH7 p.Arg3272Gln Uncertain significance ★★ ⚠ same type
DNAH7 p.Asn2116Ser Uncertain significance ★★ ⚠ same type
DNAH7 p.Asp1219Gly Uncertain significance ★★ ⚠ same type
DNAH7 p.Asp1787Gly Uncertain significance ★★ same type
DNAH7 p.Asp2867Tyr Uncertain significance ★★ ⚠ same type
DNAH7 p.Ile1203Met Uncertain significance ★★ ⚠ same type
DNAH7 p.Leu1715Met 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/dnah7-p-arg3772thr (accessed [today's date]).

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