Is DNAH7 p.Ser1856= (c.5568C>T) pathogenic?

DNAH7 p.Ser1856= (c.5568C>T) is classified Benign in DNAH7 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-11-06). Common (popmax 17.8%, afr) — too common for a highly-penetrant pathogenic allele; Associated with DNAH7-related disorder.

What condition is associated with DNAH7 p.Ser1856= (c.5568C>T)?

DNAH7 p.Ser1856= (c.5568C>T) is associated with DNAH7-related disorder (ClinVar).

DNAH7 p.Ser1856=

Q: How common is DNAH7 p.Ser1856= (c.5568C>T) in the general population?

DNAH7 p.Ser1856= (c.5568C>T) is common (popmax 17.8%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.5568C>T · rs60214909 · VCV3060172

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 17.8%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

DNAH7-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.30	acceptor loss · deltas
Pangolin	Δ0.31	gain · loss 0.23 · SpliceAI calls loss · independent
Constraint at this position
Conservation	phyloP -0.41	GERP -3.8
Overall
CADD	7.362	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 17.8% African / African-American · 13,350/74,932 alleles

Filtering AF 17.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 17.5%

Overall 12.2% 197,480/1,612,592 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	17.8%	6
Middle Eastern	17.8%	6
Ashkenazi Jewishnot grpmax-eligible	14.7%	7
European (non-Finnish)	13%	8
Amishnot grpmax-eligible	12.1%	8
Remaining individualsnot grpmax-eligible	11.9%	8
South Asian	9.14%	11
Finnishnot grpmax-eligible	8.32%	12
Admixed American	7.95%	13
East Asian	0.0379%	2,638

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.Ser1856=
Coding: c.5568C>T
MANE Select: NM_018897
dbSNP: rs60214909
Type: single nucleotide variant
Location: chr2:195884780 (GRCh38)
Gene constraint: LOEUF 0.961 · pLI <0.01 (gnomAD)

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

Disease context

DNAH7-related disorder

Similar variants

DNAH7 p.Glu3626= Uncertain significance ★ same condition
DNAH7 p.Val827Ile Uncertain significance ★ ⚠ same condition
DNAH7 p.Ala1739Thr Uncertain significance ⚠ same condition
DNAH7 p.Arg691Trp Uncertain significance same condition
DNAH7 c.1173+4A>C Likely benign same condition
DNAH7 c.6118-10T>G Likely benign same condition
DNAH7 c.7507-6A>T Likely benign same condition
DNAH7 c.*9C>T 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/dnah7-p-ser1856 (accessed [today's date]).

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