19-10987736-C-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_003072.5(SMARCA4):c.930C>A(p.Arg310Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,605,658 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0078 ( 15 hom., cov: 32)
Exomes 𝑓: 0.00078 ( 18 hom. )
Consequence
SMARCA4
NM_003072.5 synonymous
NM_003072.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.345
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 -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 19-10987736-C-A is Benign according to our data. Variant chr19-10987736-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 126367.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-10987736-C-A is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0078 (1187/152276) while in subpopulation AFR AF= 0.0274 (1138/41544). AF 95% confidence interval is 0.0261. There are 15 homozygotes in gnomad4. There are 555 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1187 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCA4 | ENST00000646693.2 | c.930C>A | p.Arg310Arg | synonymous_variant | Exon 6 of 36 | NM_001387283.1 | ENSP00000495368.1 | |||
SMARCA4 | ENST00000344626.10 | c.930C>A | p.Arg310Arg | synonymous_variant | Exon 6 of 35 | 1 | NM_003072.5 | ENSP00000343896.4 | ||
SMARCA4 | ENST00000643549.1 | c.930C>A | p.Arg310Arg | synonymous_variant | Exon 6 of 35 | ENSP00000493975.1 | ||||
SMARCA4 | ENST00000541122.6 | c.930C>A | p.Arg310Arg | synonymous_variant | Exon 7 of 35 | 5 | ENSP00000445036.2 | |||
SMARCA4 | ENST00000643296.1 | c.930C>A | p.Arg310Arg | synonymous_variant | Exon 6 of 34 | ENSP00000496635.1 | ||||
SMARCA4 | ENST00000644737.1 | c.930C>A | p.Arg310Arg | synonymous_variant | Exon 6 of 34 | ENSP00000495548.1 | ||||
SMARCA4 | ENST00000589677.5 | c.930C>A | p.Arg310Arg | synonymous_variant | Exon 7 of 35 | 5 | ENSP00000464778.1 | |||
SMARCA4 | ENST00000643995.1 | c.342C>A | p.Arg114Arg | synonymous_variant | Exon 3 of 32 | ENSP00000496004.1 |
Frequencies
GnomAD3 genomes AF: 0.00779 AC: 1186AN: 152160Hom.: 15 Cov.: 32
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GnomAD3 exomes AF: 0.00194 AC: 441AN: 227472Hom.: 5 AF XY: 0.00134 AC XY: 168AN XY: 125116
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GnomAD4 exome AF: 0.000780 AC: 1133AN: 1453382Hom.: 18 Cov.: 33 AF XY: 0.000670 AC XY: 484AN XY: 722510
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GnomAD4 genome AF: 0.00780 AC: 1187AN: 152276Hom.: 15 Cov.: 32 AF XY: 0.00745 AC XY: 555AN XY: 74456
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 13, 2021 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 22, 2023 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jun 30, 2021 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Intellectual disability, autosomal dominant 16 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Rhabdoid tumor predisposition syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 04, 2025 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 20, 2015 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Coffin-Siris syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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