ESPN c.2061+7G>A
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.683%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.18 | GERP 0.17 |
| Non-coding constraint | Z 4.31 | 1 kb window · o/e 0.70 · regional · uncalibrated |
| Overall | ||
| CADD | 7.131 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.683%
South Asian · 620/90,776 alleles
Filtering AF
0.638%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.621%
Overall
0.0686%
1,105/1,611,518 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.683% | 146 |
| Ashkenazi Jewishnot grpmax-eligible | 0.217% | 461 |
| Middle Eastern | 0.154% | 650 |
| Remaining individualsnot grpmax-eligible | 0.0834% | 1,199 |
| European (non-Finnish) | 0.0291% | 3,439 |
| Finnishnot grpmax-eligible | 0.0127% | 7,857 |
| African / African-American | 0.00533% | 18,760 |
| Admixed American | 0.00501% | 19,947 |
| East Asian | 0.00446% | 22,416 |
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
- ESPN
- Coding
- c.2061+7G>A
- MANE Select
- NM_031475
- dbSNP
- rs369405672
- Type
- single nucleotide variant
- Location
- chr1:6451755 (GRCh38)
- Gene constraint
- LOEUF 1.307 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.76
Similar variants
- ESPN c.1464+1G>A Likely pathogenic ★★ same type
- ESPN p.Ala139Thr Uncertain significance ★★ ⚠ same type
- ESPN p.Ala23Thr Uncertain significance ★★ ⚠ same type
- ESPN p.Ala484Thr Uncertain significance ★★ ⚠ same type
- ESPN p.Ala591Val Uncertain significance ★★ ⚠ same type
- ESPN p.Ala610Pro Uncertain significance ★★ ⚠ same type
- ESPN p.Ala624Thr Uncertain significance ★★ ⚠ same type
- ESPN p.Ala729Glu 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/espn-c-2061-plus-7g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown