SCD p.Lys68=
c.204G>A · rs61733935 · VCV787080
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.897%, 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 3.8 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 12.89 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.897%
African / African-American · 673/75,012 alleles
Filtering AF
0.841%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.819%
Overall
0.0455%
735/1,614,144 alleles · rare
exomes 354/1,461,884 · genomes 381/152,260 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.897% | 111 |
| Remaining individualsnot grpmax-eligible | 0.0544% | 1,839 |
| Admixed American | 0.04% | 2,501 |
| European (non-Finnish) | 0.000339% | 295,010 |
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
- SCD
- Protein
- p.Lys68=
- Coding
- c.204G>A
- MANE Select
- NM_005063
- dbSNP
- rs61733935
- Type
- single nucleotide variant
- Location
- chr10:100348240 (GRCh38)
- Gene constraint
- LOEUF 0.242 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 90.01 · 1 PDB
Similar variants
- SCD p.Lys68Met Uncertain significance ★ ⚠ same residue
- SCD p.Tyr308= Benign ★★ same type
- SCD p.Ala292Ser Uncertain significance ★ ⚠ same type
- SCD p.Ala328Val Uncertain significance ★ ⚠ same type
- SCD p.Arg155Gly Uncertain significance ★ ⚠ same type
- SCD p.Gln243His Uncertain significance ★ ⚠ same type
- SCD p.Gln29Lys Uncertain significance ★ ⚠ same type
- SCD p.Gly352Arg 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/scd-p-lys68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown