MEF2A p.Ser415=
c.1245G>A · rs3730059 · VCV3056101
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.43%, nfe)
Conditions
1
MEF2A-related disorder
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 0.017 | phastCons 0.061 |
| Overall | ||
| CADD | 5.486 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.43%
European (non-Finnish) · 39,227/1,144,972 alleles
Filtering AF
3.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.39%
Overall
2.84%
43,886/1,544,880 alleles · low-frequency
exomes 40,823/1,399,330 · genomes 3,063/145,550 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 3.43% | 29 |
| Remaining individualsnot grpmax-eligible | 2.74% | 37 |
| Admixed American | 1.94% | 51 |
| Ashkenazi Jewishnot grpmax-eligible | 1.67% | 60 |
| Finnishnot grpmax-eligible | 1.61% | 62 |
| Middle Eastern | 0.936% | 107 |
| African / African-American | 0.529% | 189 |
| South Asian | 0.214% | 467 |
| East Asian | 0.00741% | 13,503 |
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
- MEF2A
- Protein
- p.Ser415=
- Coding
- c.1245G>A
- MANE Select
- NM_001319206
- dbSNP
- rs3730059
- Type
- single nucleotide variant
- Location
- chr15:99712498 (GRCh38)
- Gene constraint
- LOEUF 0.762 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.90 · 10 PDB
Disease context
MEF2A-related disorder
Similar variants
- MEF2A p.Gly281Asp Pathogenic same condition
- MEF2A c.611-8G>A Benign same condition
- MEF2A p.Asn295= Benign same condition
- MEF2A p.Gln297= Benign same condition
- MEF2A p.Gly449= Benign same condition
- MEF2A p.Pro429Gln Likely benign same condition
- MEF2A p.Pro478= Benign same condition
- MEF2A p.Gln424_Gln428del Benign same condition
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/mef2a-p-ser415 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown