rs1351249230
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003072.5(SMARCA4):c.-32+34C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000202 in 148,442 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 31)
Consequence
SMARCA4
NM_003072.5 intron
NM_003072.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.880
Genes affected
SMARCA4 (HGNC:11100): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4) The protein encoded by this gene is a member of the SWI/SNF family of proteins and is similar to the brahma protein of Drosophila. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. In addition, this protein can bind BRCA1, as well as regulate the expression of the tumorigenic protein CD44. Mutations in this gene cause rhabdoid tumor predisposition syndrome type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.27).
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SMARCA4 | ENST00000646693.2 | c.-29+34C>A | intron_variant | Intron 1 of 35 | NM_001387283.1 | ENSP00000495368.1 | ||||
| SMARCA4 | ENST00000344626.10 | c.-32+34C>A | intron_variant | Intron 1 of 34 | 1 | NM_003072.5 | ENSP00000343896.4 | |||
| SMARCA4 | ENST00000643549.1 | c.-29+34C>A | intron_variant | Intron 1 of 34 | ENSP00000493975.1 | |||||
| SMARCA4 | ENST00000541122.6 | c.-192+34C>A | intron_variant | Intron 1 of 34 | 5 | ENSP00000445036.2 | ||||
| SMARCA4 | ENST00000643296.1 | c.-32+34C>A | intron_variant | Intron 1 of 33 | ENSP00000496635.1 | |||||
| SMARCA4 | ENST00000644737.1 | c.-29+34C>A | intron_variant | Intron 1 of 33 | ENSP00000495548.1 | |||||
| SMARCA4 | ENST00000589677.5 | c.-261+34C>A | intron_variant | Intron 1 of 34 | 5 | ENSP00000464778.1 |
Frequencies
GnomAD3 genomes 0.0000202 AC: 3AN: 148442Hom.: 0 Cov.: 31
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GnomAD4 genome 0.0000202 AC: 3AN: 148442Hom.: 0 Cov.: 31 AF XY: 0.0000415 AC XY: 3AN XY: 72326
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ClinVar
Not reported inComputational scores
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Name
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Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at