rs1555755067
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_003072.5(SMARCA4):c.982_986delCCGCA(p.Pro328AspfsTer57) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_003072.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMARCA4 | NM_001387283.1 | c.982_986delCCGCA | p.Pro328AspfsTer57 | frameshift_variant | Exon 6 of 36 | ENST00000646693.2 | NP_001374212.1 | |
SMARCA4 | NM_003072.5 | c.982_986delCCGCA | p.Pro328AspfsTer57 | frameshift_variant | Exon 6 of 35 | ENST00000344626.10 | NP_003063.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCA4 | ENST00000646693.2 | c.982_986delCCGCA | p.Pro328AspfsTer57 | frameshift_variant | Exon 6 of 36 | NM_001387283.1 | ENSP00000495368.1 | |||
SMARCA4 | ENST00000344626.10 | c.982_986delCCGCA | p.Pro328AspfsTer57 | frameshift_variant | Exon 6 of 35 | 1 | NM_003072.5 | ENSP00000343896.4 | ||
SMARCA4 | ENST00000643549.1 | c.982_986delCCGCA | p.Pro328AspfsTer57 | frameshift_variant | Exon 6 of 35 | ENSP00000493975.1 | ||||
SMARCA4 | ENST00000541122.6 | c.982_986delCCGCA | p.Pro328AspfsTer57 | frameshift_variant | Exon 7 of 35 | 5 | ENSP00000445036.2 | |||
SMARCA4 | ENST00000643296.1 | c.982_986delCCGCA | p.Pro328AspfsTer57 | frameshift_variant | Exon 6 of 34 | ENSP00000496635.1 | ||||
SMARCA4 | ENST00000644737.1 | c.982_986delCCGCA | p.Pro328AspfsTer57 | frameshift_variant | Exon 6 of 34 | ENSP00000495548.1 | ||||
SMARCA4 | ENST00000589677.5 | c.982_986delCCGCA | p.Pro328AspfsTer57 | frameshift_variant | Exon 7 of 35 | 5 | ENSP00000464778.1 | |||
SMARCA4 | ENST00000643995.1 | c.394_398delCCGCA | p.Pro132fs | frameshift_variant | Exon 3 of 32 | ENSP00000496004.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Rhabdoid tumor predisposition syndrome 2 Pathogenic:1
This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SMARCA4-related disease. Loss-of-function variants in SMARCA4 are known to be pathogenic (PMID: 24658001, 24658002). For these reasons, this variant has been classified as Pathogenic. This sequence change creates a premature translational stop signal (p.Pro328Aspfs*57) in the SMARCA4 gene. It is expected to result in an absent or disrupted protein product. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at