HAND2 p.Pro8=
c.24C>T · rs536958034 · VCV1673213
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.17%, 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 2.4 | GERP -2.3, phastCons 1 |
| Overall | ||
| CADD | 9.964 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.17%
African / African-American · 765/65,236 alleles
Filtering AF
1.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.08%
Overall
0.0642%
878/1,368,546 alleles · low-frequency
exomes 351/1,217,272 · genomes 527/151,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.17% | 85 |
| Admixed American | 0.192% | 520 |
| Remaining individualsnot grpmax-eligible | 0.0844% | 1,185 |
| Middle Eastern | 0.0684% | 1,461 |
| European (non-Finnish) | 0.0015% | 66,870 |
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
- HAND2
- Protein
- p.Pro8=
- Coding
- c.24C>T
- MANE Select
- NM_021973
- dbSNP
- rs536958034
- Type
- single nucleotide variant
- Location
- chr4:173529266 (GRCh38)
- Gene constraint
- LOEUF 0.601 · pLI 0.89 (gnomAD)
- Structure
- AlphaFold pLDDT 67.30
Similar variants
- HAND2 p.Pro8Leu Uncertain significance ★ ⚠ same residue
- HAND2 p.Pro8Ser Uncertain significance ★ ⚠ same residue
- HAND2 p.Glu38Gln Uncertain significance ★★ same type
- HAND2 p.Gly162Ser Uncertain significance ★★ ⚠ same type
- HAND2 p.Gly74Ser Uncertain significance ★★ ⚠ same type
- HAND2 p.Lys216Asn Uncertain significance ★★ ⚠ same type
- HAND2 c.556-18C>G Benign/Likely benign ★★ same type
- HAND2 p.Ala164= 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/hand2-p-pro8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown