Is DNAH7 p.Arg2875Ter (c.8623C>T) pathogenic?

DNAH7 p.Arg2875Ter (c.8623C>T) is classified Likely benign in DNAH7 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). Rare (popmax 0.151%, eas).

How common is DNAH7 p.Arg2875Ter (c.8623C>T) in the general population?

DNAH7 p.Arg2875Ter (c.8623C>T) is rare (popmax 0.151%, eas) (gnomAD).

DNAH7 p.Arg2875Ter

c.8623C>T · rs139835496 · VCV733396

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.151%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 46 of 65
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP 0.089, phastCons 0.98
Overall
CADD	40.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.151% East Asian · 67/44,518 alleles

Filtering AF 0.122% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.111%

Overall 0.00945% 152/1,607,952 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.151%	664
Remaining individualsnot grpmax-eligible	0.09%	1,111
South Asian	0.00334%	29,975
European (non-Finnish)	0.00212%	47,083
African / African-American	0.00134%	74,726

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.Arg2875Ter
Coding: c.8623C>T
MANE Select: NM_018897
dbSNP: rs139835496
Type: single nucleotide variant
Location: chr2:195853501 (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

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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-arg2875ter (accessed [today's date]).

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