19-11058901-G-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003072.5(SMARCA4):c.4635+12G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000962 in 1,455,764 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Consequence
SMARCA4
NM_003072.5 intron
NM_003072.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.18
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 Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 19-11058901-G-T is Benign according to our data. Variant chr19-11058901-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1558259.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 14 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCA4 | ENST00000646693.2 | c.4731+12G>T | intron_variant | Intron 33 of 35 | NM_001387283.1 | ENSP00000495368.1 | ||||
SMARCA4 | ENST00000344626.10 | c.4635+12G>T | intron_variant | Intron 32 of 34 | 1 | NM_003072.5 | ENSP00000343896.4 | |||
SMARCA4 | ENST00000643549.1 | c.4641+12G>T | intron_variant | Intron 32 of 34 | ENSP00000493975.1 | |||||
SMARCA4 | ENST00000541122.6 | c.4545+12G>T | intron_variant | Intron 32 of 34 | 5 | ENSP00000445036.2 | ||||
SMARCA4 | ENST00000643296.1 | c.4545+12G>T | intron_variant | Intron 31 of 33 | ENSP00000496635.1 | |||||
SMARCA4 | ENST00000644737.1 | c.4545+12G>T | intron_variant | Intron 31 of 33 | ENSP00000495548.1 | |||||
SMARCA4 | ENST00000589677.5 | c.4542+12G>T | intron_variant | Intron 32 of 34 | 5 | ENSP00000464778.1 | ||||
SMARCA4 | ENST00000643995.1 | c.4056+12G>T | intron_variant | Intron 29 of 31 | ENSP00000496004.1 | |||||
SMARCA4 | ENST00000644963.1 | c.3285+12G>T | intron_variant | Intron 25 of 27 | ENSP00000495599.1 | |||||
SMARCA4 | ENST00000644065.1 | c.3267+12G>T | intron_variant | Intron 24 of 26 | ENSP00000493615.1 | |||||
SMARCA4 | ENST00000642350.1 | c.3129+12G>T | intron_variant | Intron 24 of 26 | ENSP00000495355.1 | |||||
SMARCA4 | ENST00000643857.1 | c.2895+538G>T | intron_variant | Intron 22 of 24 | ENSP00000494159.1 | |||||
SMARCA4 | ENST00000538456.4 | c.699+538G>T | intron_variant | Intron 5 of 7 | 3 | ENSP00000495197.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000962 AC: 14AN: 1455764Hom.: 0 Cov.: 29 AF XY: 0.00000966 AC XY: 7AN XY: 724582
GnomAD4 exome
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14
AN:
1455764
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Cov.:
29
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AC XY:
7
AN XY:
724582
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Rhabdoid tumor predisposition syndrome 2 Benign:1
Jul 03, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Calibrated prediction
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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
Publications
No publications associated with this variant yet.