rs797045275
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP3BP6_Very_StrongBS2
The NM_001374828.1(ARID1B):c.612_623delACAGCAGCAGCA(p.Gln205_Gln208del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000422 in 1,541,304 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. QQ204Q?) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000040 ( 0 hom. )
Consequence
ARID1B
NM_001374828.1 disruptive_inframe_deletion
NM_001374828.1 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.85
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 Benign. Variant got -13 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001374828.1
BP6
Variant 6-156778280-GCAGCAGCAGCAA-G is Benign according to our data. Variant chr6-156778280-GCAGCAGCAGCAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 210286.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 10 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARID1B | NM_001374828.1 | c.612_623delACAGCAGCAGCA | p.Gln205_Gln208del | disruptive_inframe_deletion | 1/20 | ENST00000636930.2 | NP_001361757.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARID1B | ENST00000636930.2 | c.612_623delACAGCAGCAGCA | p.Gln205_Gln208del | disruptive_inframe_deletion | 1/20 | 2 | NM_001374828.1 | ENSP00000490491.2 |
Frequencies
GnomAD3 genomes AF: 0.0000660 AC: 10AN: 151588Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.0000396 AC: 55AN: 1389716Hom.: 0 AF XY: 0.0000394 AC XY: 27AN XY: 685570
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GnomAD4 genome AF: 0.0000660 AC: 10AN: 151588Hom.: 0 Cov.: 31 AF XY: 0.0000675 AC XY: 5AN XY: 74056
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 22, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 20, 2023 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at