rs1112534
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003070.5(SMARCA2):c.226-107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 974,010 control chromosomes in the GnomAD database, including 22,322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.23 ( 4252 hom., cov: 32)
Exomes 𝑓: 0.20 ( 18070 hom. )
Consequence
SMARCA2
NM_003070.5 intron
NM_003070.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.372
Genes affected
SMARCA2 (HGNC:11098): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2) The protein encoded by this gene is a member of the SWI/SNF family of proteins and is highly 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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, which contains a trinucleotide repeat (CAG) length polymorphism. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 9-2032845-G-A is Benign according to our data. Variant chr9-2032845-G-A is described in ClinVar as [Benign]. Clinvar id is 1235432.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCA2 | NM_003070.5 | c.226-107G>A | intron_variant | ENST00000349721.8 | |||
SMARCA2 | NM_001289396.1 | c.226-107G>A | intron_variant | ||||
SMARCA2 | NM_001289397.2 | c.226-107G>A | intron_variant | ||||
SMARCA2 | NM_139045.4 | c.226-107G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCA2 | ENST00000349721.8 | c.226-107G>A | intron_variant | 5 | NM_003070.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.229 AC: 34791AN: 151992Hom.: 4233 Cov.: 32
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GnomAD4 exome AF: 0.204 AC: 167310AN: 821900Hom.: 18070 AF XY: 0.200 AC XY: 84187AN XY: 420880
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GnomAD4 genome ? AF: 0.229 AC: 34846AN: 152110Hom.: 4252 Cov.: 32 AF XY: 0.232 AC XY: 17270AN XY: 74378
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 03, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at