Is SBF1 p.Asp6= (c.18C>T) pathogenic?

SBF1 p.Asp6= (c.18C>T) is classified Likely benign in SBF1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-02-06). Ultra-rare (popmax 0.0239%, afr).

How common is SBF1 p.Asp6= (c.18C>T) in the general population?

SBF1 p.Asp6= (c.18C>T) is ultra-rare (popmax 0.0239%, afr) (gnomAD).

SBF1 p.Asp6=

c.18C>T · rs1010989734 · VCV1190144

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0239%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 6.2	GERP -0.68, phastCons 1
Overall
CADD	14.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0239% African / African-American · 16/67,040 alleles

Filtering AF 0.0149% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0122%

Overall 0.00133% 19/1,425,992 alleles · ultra-rare exomes 7/1,275,986 · genomes 12/150,006 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0239%	4,190
Remaining individualsnot grpmax-eligible	0.00369%	27,091
Admixed American	0.00258%	38,696

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: SBF1
Protein: p.Asp6=
Coding: c.18C>T
MANE Select: NM_002972
dbSNP: rs1010989734
Type: single nucleotide variant
Location: chr22:50474823 (GRCh38)
Gene constraint: LOEUF 0.381 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 74.72

Full SBF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SBF1 c.3826+1G>A Pathogenic/Likely pathogenic ★★ same type
SBF1 p.Met417Val Pathogenic/Likely pathogenic ★★ ⚠ same type
SBF1 c.1431+6A>T Uncertain significance ★★ same type
SBF1 c.1636+4C>T Uncertain significance ★★ same type
SBF1 c.1899+3G>A Uncertain significance ★★ same type
SBF1 c.2643+6C>T Uncertain significance ★★ same type
SBF1 c.279+3C>T Uncertain significance ★★ same type
SBF1 c.3904+6G>A 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/sbf1-p-asp6 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown