rs797045268
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_001374828.1(ARID1B):βc.1312_1320delβ(p.Gly438_Gly440del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,262,838 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (β ).
Frequency
Genomes: π 0.000015 ( 0 hom., cov: 29)
Exomes π: 0.000036 ( 1 hom. )
Consequence
ARID1B
NM_001374828.1 inframe_deletion
NM_001374828.1 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.82
Genes affected
ARID1B (HGNC:18040): (AT-rich interaction domain 1B) This locus encodes an AT-rich DNA interacting domain-containing protein. The encoded protein is a component of the SWI/SNF chromatin remodeling complex and may play a role in cell-cycle activation. The protein encoded by this locus is similar to AT-rich interactive domain-containing protein 1A. These two proteins function as alternative, mutually exclusive ARID-subunits of the SWI/SNF complex. The associated complexes play opposing roles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
?
Nonframeshift variant in repetitive region in NM_001374828.1
BS2
?
High AC in GnomAdExome4 at 41 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1B | NM_001374828.1 | c.1312_1320del | p.Gly438_Gly440del | inframe_deletion | 1/20 | ENST00000636930.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1B | ENST00000636930.2 | c.1312_1320del | p.Gly438_Gly440del | inframe_deletion | 1/20 | 2 | NM_001374828.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000146 AC: 2AN: 137298Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 0.0000364 AC: 41AN: 1125434Hom.: 1 AF XY: 0.0000461 AC XY: 25AN XY: 541872
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GnomAD4 genome ? AF: 0.0000146 AC: 2AN: 137404Hom.: 0 Cov.: 29 AF XY: 0.0000297 AC XY: 2AN XY: 67288
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | This variant, c.1063_1071del, results in the deletion of 3 amino acid(s) of the ARID1B protein (p.Gly355_Gly357del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with ARID1B-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at