EDAR c.1024+147T>C
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 7.12%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +147 | deep intronic (+147 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -2 |
| Overall | ||
| CADD | 0.144 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.12%
African / African-American · 4,116/57,836 alleles
Filtering AF
6.94%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.86%
Overall
0.601%
4,641/771,622 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 7.12% | 14 |
| Admixed American | 0.614% | 163 |
| Remaining individualsnot grpmax-eligible | 0.551% | 181 |
| Middle Eastern | 0.249% | 402 |
| South Asian | 0.00898% | 11,132 |
| European (non-Finnish) | 0.00744% | 13,435 |
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
- EDAR
- Coding
- c.1024+147T>C
- MANE Select
- NM_022336
- dbSNP
- rs17037091
- Type
- single nucleotide variant
- Location
- chr2:108906161 (GRCh38)
- Gene constraint
- LOEUF 0.927 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.01 · 1 PDB
Similar variants
- EDAR c.730+1G>T Pathogenic ★★ same type
- EDAR p.Ala26Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- EDAR p.Arg25Ter Pathogenic/Likely pathogenic ★★ same type
- EDAR p.Arg358Ter Pathogenic ★★ same type
- EDAR p.Arg420Gln Pathogenic/Likely pathogenic ★★ same type
- EDAR p.Arg89His Pathogenic/Likely pathogenic ★★ ⚠ same type
- EDAR p.Arg98Trp Pathogenic/Likely pathogenic ★★ same type
- EDAR p.Cys148Arg Likely pathogenic ★★ 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/edar-c-1024-plus-147t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown