CHD2 c.1719+71C>T
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 97%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +71 | deep intronic (+71 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.38 | GERP -5.2 |
| Non-coding constraint | Z 3.95 | 1 kb window · o/e 0.65 · regional · uncalibrated |
| Overall | ||
| CADD | 5.626 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
97%
East Asian · 42,393/43,682 alleles
Filtering AF
96.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 96%
Overall
79.8%
1,124,406/1,409,694 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 97% | 1 |
| Amishnot grpmax-eligible | 92.1% | 1 |
| Admixed American | 88.5% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 86.4% | 1 |
| Middle Eastern | 81.7% | 1 |
| European (non-Finnish) | 80.6% | 1 |
| Remaining individualsnot grpmax-eligible | 79.6% | 1 |
| South Asian | 77.1% | 1 |
| Finnishnot grpmax-eligible | 73.8% | 1 |
| African / African-American | 55.4% | 2 |
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
- CHD2
- Coding
- c.1719+71C>T
- MANE Select
- NM_001271
- dbSNP
- rs1371390
- Type
- single nucleotide variant
- Location
- chr15:92953644 (GRCh38)
- Gene constraint
- LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.81
Similar variants
- CHD2 c.1153+1G>C Pathogenic ★★ same type
- CHD2 c.1809+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHD2 c.294+1G>T Likely pathogenic ★★ same type
- CHD2 c.443+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHD2 c.693-1G>A Likely pathogenic ★★ same type
- CHD2 p.Ala879Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- CHD2 p.Arg1072Ter Pathogenic ★★ same type
- CHD2 p.Arg1137Ter Pathogenic/Likely pathogenic ★★ 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/chd2-c-1719-plus-71c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown