GIT1 p.Asn706=
c.2118C>T · VCV4934409
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00561%, 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 -6.5 | GERP -3.5 |
| Overall | ||
| CADD | 4.932 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00561%
South Asian · 5/89,192 alleles
Filtering AF
0.00214%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00139%
Overall
0.0017%
27/1,587,198 alleles · very rare
exomes 26/1,435,012 · genomes 1/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00561% | 17,838 |
| European (non-Finnish) | 0.00188% | 53,174 |
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
- GIT1
- Protein
- p.Asn706=
- Coding
- c.2118C>T
- MANE Select
- NM_014030
- Type
- single nucleotide variant
- Location
- chr17:29574870 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
- Residue 706
- the 'interaction with pxn and tgfb1i1' region
Similar variants
- GIT1 p.Pro83= Benign ★★ same type
- GIT1 c.762-205C>T Uncertain significance ★ same type
- GIT1 p.Ala130Thr Uncertain significance ★ ⚠ same type
- GIT1 p.Ala183Gly Uncertain significance ★ same type
- GIT1 p.Ala311Val Uncertain significance ★ ⚠ same type
- GIT1 p.Ala402Thr Uncertain significance ★ ⚠ same type
- GIT1 p.Ala466Val Uncertain significance ★ ⚠ same type
- GIT1 p.Ala488Thr 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/git1-p-asn706 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown