Is SMARCB1 p.Asp22= (c.66C>T) pathogenic?

SMARCB1 p.Asp22= (c.66C>T) is classified Likely benign in SMARCB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-08). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with SMARCB1 p.Asp22= (c.66C>T)?

SMARCB1 p.Asp22= (c.66C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is SMARCB1 p.Asp22= (c.66C>T) in the general population?

SMARCB1 p.Asp22= (c.66C>T) is absent from gnomAD v4.1 (gnomAD).

SMARCB1 p.Asp22=

c.66C>T · VCV3446071

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.56 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.19	GERP 0.37, phastCons 0.38
Overall
CADD	12.39	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SMARCB1
Protein: p.Asp22=
Coding: c.66C>T
MANE Select: NM_003073
Type: single nucleotide variant
Location: chr22:23787235 (GRCh38)
Gene constraint: LOEUF 0.221 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 80.77 · 17 PDB
Residue 22: the 'dna-binding' region

Full SMARCB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SMARCB1 p.Asp22Asn Uncertain significance ★★ ⚠ same residue
SMARCB1 p.Asp22His Uncertain significance ★★ same residue
SMARCB1 c.795+1G>A Likely pathogenic ★★ same condition
SMARCB1 c.93+1G>A Likely pathogenic ★★ same condition
SMARCB1 c.986+1G>A Likely pathogenic ★★ same condition
SMARCB1 c.*82C>T Pathogenic/Likely pathogenic ★★ same condition
SMARCB1 p.Arg158Ter Pathogenic ★★ same condition
SMARCB1 p.Arg201Ter Pathogenic ★★ same condition

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/smarcb1-p-asp22 (accessed [today's date]).

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