NM_001387283.1:c.2616+2_2616+5dupTAAC
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001387283.1(SMARCA4):c.2616+2_2616+5dupTAAC variant causes a splice region, intron 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 Uncertain significance (★).
Frequency
Consequence
NM_001387283.1 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMARCA4 | NM_001387283.1 | c.2616+2_2616+5dupTAAC | splice_region_variant, intron_variant | Intron 18 of 35 | ENST00000646693.2 | NP_001374212.1 | ||
SMARCA4 | NM_003072.5 | c.2616+2_2616+5dupTAAC | splice_region_variant, intron_variant | Intron 18 of 34 | ENST00000344626.10 | NP_003063.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCA4 | ENST00000646693.2 | c.2616+1_2616+2insTAAC | splice_donor_variant, intron_variant | Intron 18 of 35 | NM_001387283.1 | ENSP00000495368.1 | ||||
SMARCA4 | ENST00000344626.10 | c.2616+1_2616+2insTAAC | splice_donor_variant, intron_variant | Intron 18 of 34 | 1 | NM_003072.5 | ENSP00000343896.4 | |||
SMARCA4 | ENST00000643549.1 | c.2616+1_2616+2insTAAC | splice_donor_variant, intron_variant | Intron 18 of 34 | ENSP00000493975.1 | |||||
SMARCA4 | ENST00000541122.6 | c.2616+1_2616+2insTAAC | splice_donor_variant, intron_variant | Intron 19 of 34 | 5 | ENSP00000445036.2 | ||||
SMARCA4 | ENST00000643296.1 | c.2616+1_2616+2insTAAC | splice_donor_variant, intron_variant | Intron 18 of 33 | ENSP00000496635.1 | |||||
SMARCA4 | ENST00000644737.1 | c.2616+1_2616+2insTAAC | splice_donor_variant, intron_variant | Intron 18 of 33 | ENSP00000495548.1 | |||||
SMARCA4 | ENST00000589677.5 | c.2616+1_2616+2insTAAC | splice_donor_variant, intron_variant | Intron 19 of 34 | 5 | ENSP00000464778.1 | ||||
SMARCA4 | ENST00000643995.1 | c.2028+1_2028+2insTAAC | splice_donor_variant, intron_variant | Intron 15 of 31 | ENSP00000496004.1 | |||||
SMARCA4 | ENST00000644963.1 | c.1260+1_1260+2insTAAC | splice_donor_variant, intron_variant | Intron 11 of 27 | ENSP00000495599.1 | |||||
SMARCA4 | ENST00000644065.1 | c.1341+1_1341+2insTAAC | splice_donor_variant, intron_variant | Intron 11 of 26 | ENSP00000493615.1 | |||||
SMARCA4 | ENST00000642350.1 | c.1101+1_1101+2insTAAC | splice_donor_variant, intron_variant | Intron 10 of 26 | ENSP00000495355.1 | |||||
SMARCA4 | ENST00000643857.1 | c.969+1_969+2insTAAC | splice_donor_variant, intron_variant | Intron 9 of 24 | ENSP00000494159.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 28
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Rhabdoid tumor predisposition syndrome 2 Uncertain:1
This sequence change falls in intron 18 of the SMARCA4 gene. It does not directly change the encoded amino acid sequence of the SMARCA4 protein, but it affects a nucleotide within the consensus splice site of the intron. 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. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at