Is DNAH7 p.Thr3307Ser (c.9920C>G) pathogenic?

DNAH7 p.Thr3307Ser (c.9920C>G) is classified Likely benign in DNAH7 (ClinVar, Single submitter, 2 submitters; last evaluated 2023-02-01). AlphaMissense: ambiguous (0.4075); Rare (popmax 0.512%, mid).

How common is DNAH7 p.Thr3307Ser (c.9920C>G) in the general population?

DNAH7 p.Thr3307Ser (c.9920C>G) is rare (popmax 0.512%, mid) (gnomAD).

What do computational predictors say about DNAH7 p.Thr3307Ser (c.9920C>G)?

AlphaMissense predicts ambiguous (score 0.4075) — an in-silico prediction, not a clinical call.

DNAH7 p.Thr3307Ser

c.9920C>G · rs144112024 · VCV2651774

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.4075 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.512%, mid)

Computational evidence

Protein change
AlphaMissense	0.4075	ambiguous
REVEL	0.336	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 331 kb · p 0.14 · regional, not allelic
Overall
CADD	24.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.512% Middle Eastern · 31/6,058 alleles

Filtering AF 0.435% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.431%

Overall 0.357% 5,760/1,613,586 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.512%	195
European (non-Finnish)	0.445%	225
Remaining individualsnot grpmax-eligible	0.266%	376
Finnishnot grpmax-eligible	0.134%	744
South Asian	0.131%	765
Admixed American	0.104%	966
African / African-American	0.06%	1,667
Ashkenazi Jewishnot grpmax-eligible	0.00676%	14,795
East Asian	0.00223%	44,848

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.Thr3307Ser
Coding: c.9920C>G
MANE Select: NM_018897
dbSNP: rs144112024
Type: single nucleotide variant
Location: chr2:195808845 (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-thr3307ser (accessed [today's date]).

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