GDF3 p.Ser102=
c.306C>T · rs574345420 · VCV779828
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.493%, sas)
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 1.5 | phastCons 0.36 |
| Overall | ||
| CADD | 2.627 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.493%
South Asian · 449/91,028 alleles
Filtering AF
0.456%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.441%
Overall
0.0288%
465/1,613,030 alleles · rare
exomes 449/1,460,830 · genomes 16/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.493% | 203 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,804 |
| Middle Eastern | 0.0165% | 6,050 |
| African / African-American | 0.00133% | 74,974 |
| European (non-Finnish) | 8.48e-05% | 1,179,258 |
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
- GDF3
- Protein
- p.Ser102=
- Coding
- c.306C>T
- MANE Select
- NM_020634
- dbSNP
- rs574345420
- Type
- single nucleotide variant
- Location
- chr12:7690667 (GRCh38)
- Gene constraint
- LOEUF 1.513 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.72
Similar variants
- GDF3 p.Arg274Trp Uncertain significance ★★ ⚠ same type
- GDF3 p.Pro325Thr Uncertain significance ★★ ⚠ same type
- GDF3 p.Ser304Pro Uncertain significance ★★ ⚠ same type
- GDF3 p.Val320Ile Uncertain significance ★★ ⚠ same type
- GDF3 c.268+117G>A Benign ★★ same type
- GDF3 c.269-73G>A Benign ★★ same type
- GDF3 p.Arg195Trp Benign/Likely benign ★★ same type
- GDF3 p.Asn193= Benign/Likely 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/gdf3-p-ser102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown