SPEN p.Arg31=
c.93C>T · rs150922162 · VCV3038799
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.462%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -5.2 |
| Overall | ||
| CADD | 0.567 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.462%
European (non-Finnish) · 5,145/1,113,786 alleles
Filtering AF
0.451%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.447%
Overall
0.367%
5,481/1,492,066 alleles · rare
exomes 5,233/1,339,880 · genomes 248/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.462% | 216 |
| Remaining individualsnot grpmax-eligible | 0.352% | 284 |
| Admixed American | 0.123% | 810 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0725% | 1,379 |
| African / African-American | 0.0668% | 1,497 |
| Finnishnot grpmax-eligible | 0.0184% | 5,432 |
| Middle Eastern | 0.0182% | 5,484 |
| South Asian | 0.00143% | 70,076 |
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
- SPEN
- Protein
- p.Arg31=
- Coding
- c.93C>T
- MANE Select
- NM_015001
- dbSNP
- rs150922162
- Type
- single nucleotide variant
- Location
- chr1:15872825 (GRCh38)
- Gene constraint
- LOEUF 0.094 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 31
- the rrm 1 domain; a DNA-binding region
Similar variants
- SPEN p.Arg31His Conflicting classifications of pathogenicity ★ same residue
- SPEN p.Arg1170Ter Pathogenic ★★ same type
- SPEN p.Arg1241Ter Pathogenic ★★ same type
- SPEN p.Arg1265Ter Pathogenic ★★ same type
- SPEN p.Arg2337Ter Likely pathogenic ★★ same type
- SPEN p.Arg2342Ter Pathogenic ★★ same type
- SPEN p.Arg308Ter Pathogenic ★★ same type
- SPEN p.Arg3168Ter 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/spen-p-arg31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown