GIT1 c.623+10G>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +10 | near-intronic (+10 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.7 | GERP -3.5 |
| Non-coding constraint | Z 4.77 | 1 kb window · o/e 0.71 · regional · uncalibrated |
| Overall | ||
| CADD | 0.131 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,078 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000605%
Overall
0.00118%
19/1,612,502 alleles · very rare
exomes 17/1,460,200 · genomes 2/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,359 |
| African / African-American | 0.00133% | 75,028 |
| European (non-Finnish) | 0.00127% | 78,645 |
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
- Coding
- c.623+10G>A
- MANE Select
- NM_014030
- Type
- single nucleotide variant
- Location
- chr17:29581917 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
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-c-623-plus-10g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown