SRCAP c.54+122C>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 10.3%, 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 +122 | deep intronic (+122 nt into the intron) |
|---|---|---|
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.23 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -0.62 | GERP -1.1 |
| Non-coding constraint | Z -1.45 | 1 kb window · o/e 1.11 · regional · uncalibrated |
| Overall | ||
| CADD | 0.771 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.3%
African / African-American · 6,317/61,552 alleles
Filtering AF
10.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.96%
Overall
0.739%
6,970/943,688 alleles · common
exomes 2,535/791,474 · genomes 4,435/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 10.3% | 10 |
| Remaining individualsnot grpmax-eligible | 0.624% | 160 |
| Admixed American | 0.487% | 205 |
| Ashkenazi Jewishnot grpmax-eligible | 0.138% | 723 |
| Middle Eastern | 0.128% | 783 |
| East Asian | 0.118% | 847 |
| South Asian | 0.0163% | 6,131 |
| European (non-Finnish) | 0.0121% | 8,263 |
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
- SRCAP
- Coding
- c.54+122C>A
- MANE Select
- NM_006662
- dbSNP
- rs73536499
- Type
- single nucleotide variant
- Location
- chr16:30701000 (GRCh38)
- Gene constraint
- LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Similar variants
- SRCAP p.Arg2329Ter Pathogenic/Likely pathogenic ★★ same type
- SRCAP p.Arg2435Ter Pathogenic/Likely pathogenic ★★ same type
- SRCAP p.Arg2444Ter Pathogenic ★★ same type
- SRCAP p.Arg2718Ter Pathogenic/Likely pathogenic ★★ same type
- SRCAP p.Arg2748Ter Pathogenic ★★ same type
- SRCAP p.Gln2407Ter Pathogenic ★★ same type
- SRCAP p.Gln2419Ter Pathogenic ★★ same type
- SRCAP p.Gln2665Ter Pathogenic/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/srcap-c-54-plus-122c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown