UTRN c.9357+124del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 19.5%, 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 +124 | deep intronic (+124 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.12 | GERP -2.2 |
| Non-coding constraint | Z 0.28 | 1 kb window · o/e 0.98 · regional · uncalibrated |
| Overall | ||
| CADD | 2.568 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
19.5%
African / African-American · 9,948/50,944 alleles
Filtering AF
19.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 19.1%
Overall
2.91%
17,917/616,178 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 19.5% | 5 |
| East Asian | 6.86% | 15 |
| Remaining individualsnot grpmax-eligible | 3.42% | 29 |
| Ashkenazi Jewishnot grpmax-eligible | 3.1% | 32 |
| Admixed American | 2.94% | 34 |
| Amishnot grpmax-eligible | 2.78% | 36 |
| Middle Eastern | 1.56% | 64 |
| European (non-Finnish) | 0.92% | 109 |
| South Asian | 0.841% | 119 |
| Finnishnot grpmax-eligible | 0.566% | 177 |
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
- UTRN
- Coding
- c.9357+124del
- MANE Select
- NM_007124
- dbSNP
- rs71673559
- Type
- Deletion
- Location
- chr6:144803262 (GRCh38)
- Gene constraint
- LOEUF 0.665 · pLI <0.01 (gnomAD)
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/utrn-c-9357-plus-124del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown