DNAH2 p.Asp3375=
c.10125C>T · rs370664116 · VCV2647386
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.493%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -3.4 |
| Overall | ||
| CADD | 3.543 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.493%
Middle Eastern · 30/6,084 alleles
Filtering AF
0.355%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.308%
Overall
0.02%
322/1,614,020 alleles · rare
exomes 302/1,461,886 · genomes 20/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.493% | 203 |
| Admixed American | 0.04% | 2,500 |
| East Asian | 0.0245% | 4,081 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0236% | 4,229 |
| European (non-Finnish) | 0.0195% | 5,131 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,681 |
| South Asian | 0.00659% | 15,182 |
| African / African-American | 0.00401% | 24,964 |
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
- DNAH2
- Protein
- p.Asp3375=
- Coding
- c.10125C>T
- MANE Select
- NM_020877
- dbSNP
- rs370664116
- Type
- single nucleotide variant
- Location
- chr17:7817665 (GRCh38)
- Gene constraint
- LOEUF 0.655 · pLI <0.01 (gnomAD)
- Residue 3375
- the 'aaa 5' region
Similar variants
- DNAH2 p.Ala1036Val Uncertain significance ★★ ⚠ same type
- DNAH2 p.Arg1533Cys Uncertain significance ★★ ⚠ same type
- DNAH2 p.Arg2538Gln Uncertain significance ★★ same type
- DNAH2 p.Arg3759His Uncertain significance ★★ ⚠ same type
- DNAH2 p.Gln2069Glu Uncertain significance ★★ same type
- DNAH2 p.Ile4043Ser Uncertain significance ★★ ⚠ same type
- DNAH2 p.Pro3819Leu Uncertain significance ★★ ⚠ same type
- DNAH2 c.10169+3G>A Benign ★★ 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/dnah2-p-asp3375 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown