SRC c.250+306del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 100%, nfe) — 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 +306 | deep intronic (+306 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.28 | GERP -1.4 |
| Non-coding constraint | Z 6.70 | 1 kb window · o/e 0.50 · regional · uncalibrated |
| Overall | ||
| CADD | 1.105 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
100%
European (non-Finnish) · 67,984/67,984 alleles
Filtering AF
99.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 99.1%
Overall
100%
152,177/152,178 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed American | 100% | 1 |
| East Asian | 100% | 1 |
| European (non-Finnish)grpmax | 100% | 1 |
| South Asian | 100% | 1 |
| Finnishnot grpmax-eligible | 100% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 100% | 1 |
| Amishnot grpmax-eligible | 100% | 1 |
| Middle Eastern | 100% | 1 |
| Remaining individualsnot grpmax-eligible | 100% | 1 |
| African / African-American | 100% | 1 |
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
- SRC
- Coding
- c.250+306del
- MANE Select
- NM_198291
- dbSNP
- rs10714592
- Type
- Deletion
- Location
- chr20:37384708 (GRCh38)
- Gene constraint
- LOEUF 0.383 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.59 · 79 PDB
Similar variants
- SRC p.Asn417fs Uncertain significance ★ same type
- SRC c.250+265_250+268del 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/src-c-250-plus-306del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown