chr9-2039776-ACAG-A
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_003070.5(SMARCA2):βc.705_707delβ(p.Gln238del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 1,427,642 control chromosomes in the GnomAD database, including 5,709 homozygotes. Variant has been reported in ClinVar as Benign (β β ). Synonymous variant affecting the same amino acid position (i.e. Q223Q) has been classified as Likely benign.
Frequency
Genomes: π 0.17 ( 2394 hom., cov: 26)
Exomes π: 0.14 ( 3315 hom. )
Consequence
SMARCA2
NM_003070.5 inframe_deletion
NM_003070.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00
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 -16 ACMG points.
BP6
Variant 9-2039776-ACAG-A is Benign according to our data. Variant chr9-2039776-ACAG-A is described in ClinVar as [Benign]. Clinvar id is 126353.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-2039776-ACAG-A is described in Lovd as [Benign]. Variant chr9-2039776-ACAG-A is described in Lovd as [Likely_benign]. Variant chr9-2039776-ACAG-A is described in Lovd as [Benign]. Variant chr9-2039776-ACAG-A is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCA2 | NM_003070.5 | c.705_707del | p.Gln238del | inframe_deletion | 4/34 | ENST00000349721.8 | |
SMARCA2 | NM_001289396.1 | c.705_707del | p.Gln238del | inframe_deletion | 4/34 | ||
SMARCA2 | NM_001289397.2 | c.705_707del | p.Gln238del | inframe_deletion | 4/33 | ||
SMARCA2 | NM_139045.4 | c.705_707del | p.Gln238del | inframe_deletion | 4/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCA2 | ENST00000349721.8 | c.705_707del | p.Gln238del | inframe_deletion | 4/34 | 5 | NM_003070.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.165 AC: 24790AN: 150198Hom.: 2377 Cov.: 26
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GnomAD4 exome AF: 0.143 AC: 183010AN: 1277344Hom.: 3315 AF XY: 0.144 AC XY: 90470AN XY: 627376
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GnomAD4 genome AF: 0.165 AC: 24843AN: 150298Hom.: 2394 Cov.: 26 AF XY: 0.168 AC XY: 12320AN XY: 73378
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 12, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 24, 2013 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | 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. - |
Nicolaides-Baraitser syndrome;C5443984:Blepharophimosis-impaired intellectual development syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 30, 2022 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at