SDF4 p.Ser35=
c.105G>A · rs144248419 · VCV780207
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.24%, afr)
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 -9.1 | GERP -4.2 |
| Overall | ||
| CADD | 0.245 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.24%
African / African-American · 933/75,054 alleles
Filtering AF
1.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.15%
Overall
0.0681%
1,099/1,613,062 alleles · low-frequency
exomes 554/1,460,770 · genomes 545/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.24% | 80 |
| Remaining individualsnot grpmax-eligible | 0.106% | 947 |
| Admixed American | 0.0983% | 1,017 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.00549% | 18,217 |
| European (non-Finnish) | 0.00288% | 34,706 |
| Finnishnot grpmax-eligible | 0.00159% | 62,950 |
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
- SDF4
- Protein
- p.Ser35=
- Coding
- c.105G>A
- MANE Select
- NM_016176
- dbSNP
- rs144248419
- Type
- single nucleotide variant
- Location
- chr1:1228668 (GRCh38)
- Gene constraint
- LOEUF 0.875 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.03
Similar variants
- SDF4 c.-11C>T Uncertain significance ★ ⚠ same type
- SDF4 c.-18G>A Uncertain significance ★ ⚠ same type
- SDF4 c.-3G>A Uncertain significance ★ ⚠ same type
- SDF4 p.Ala161Val Uncertain significance ★ ⚠ same type
- SDF4 p.Ala293Thr Uncertain significance ★ ⚠ same type
- SDF4 p.Ala348Val Uncertain significance ★ ⚠ same type
- SDF4 p.Arg109Gln Uncertain significance ★ ⚠ same type
- SDF4 p.Arg109Trp Uncertain significance ★ ⚠ 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/sdf4-p-ser35 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown