TSPAN7 p.Ser147=
c.441C>T · rs111440990 · VCV130645
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 11.5%, 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 | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.2 | GERP -5.1 |
| Overall | ||
| CADD | 2.419 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.5%
African / African-American · 6,494/56,346 alleles
Filtering AF
11.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 11.2%
Overall
0.732%
8,647/1,180,950 alleles · common
exomes 4,894/1,069,833 · genomes 3,753/111,117 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 11.5% | 9 |
| Remaining individualsnot grpmax-eligible | 1.18% | 85 |
| Admixed American | 1.02% | 98 |
| Middle Eastern | 0.659% | 152 |
| Ashkenazi Jewishnot grpmax-eligible | 0.19% | 526 |
| European (non-Finnish) | 0.124% | 809 |
| South Asian | 0.0373% | 2,680 |
| Finnishnot grpmax-eligible | 0.00223% | 44,933 |
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
- TSPAN7
- Protein
- p.Ser147=
- Coding
- c.441C>T
- MANE Select
- NM_004615
- dbSNP
- rs111440990
- Type
- single nucleotide variant
- Location
- chrX:38674316 (GRCh38)
- Structure
- AlphaFold pLDDT 89.18 · 2 PDB
Similar variants
- TSPAN7 p.Ser147Asn Uncertain significance ★ ⚠ same residue
- TSPAN7 p.Arg139Gln Uncertain significance ★★ ⚠ same type
- TSPAN7 p.Gly64Arg Uncertain significance ★★ ⚠ same type
- TSPAN7 p.Met209Thr Uncertain significance ★★ ⚠ same type
- TSPAN7 p.Ala79= Benign/Likely benign ★★ same type
- TSPAN7 p.Pro172= Benign ★★ same type
- TSPAN7 c.271-1G>T Likely pathogenic ★ same type
- TSPAN7 p.Tyr164Ter 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/tspan7-p-ser147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown