rs797045274
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP3BP6_Very_StrongBS2
The NM_001374828.1(ARID1B):βc.612_620delβ(p.Gln212_Gln214del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.0000999 in 1,540,886 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (β β ). Synonymous variant affecting the same amino acid position (i.e. Q202Q) has been classified as Likely benign.
Frequency
Genomes: π 0.00017 ( 0 hom., cov: 31)
Exomes π: 0.000092 ( 0 hom. )
Consequence
ARID1B
NM_001374828.1 inframe_deletion
NM_001374828.1 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 6-156778283-GCAGCAGCAA-G is Benign according to our data. Variant chr6-156778283-GCAGCAGCAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 210285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-156778283-GCAGCAGCAA-G is described in Lovd as [Likely_benign].
BS2
?
High AC in GnomAd4 at 26 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1B | NM_001374828.1 | c.612_620del | p.Gln212_Gln214del | inframe_deletion | 1/20 | ENST00000636930.2 | |
LOC115308161 | NR_163974.1 | n.227_235del | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1B | ENST00000636930.2 | c.612_620del | p.Gln212_Gln214del | inframe_deletion | 1/20 | 2 | NM_001374828.1 | A2 | |
ENST00000603191.2 | n.131_139del | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000172 AC: 26AN: 151524Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000234 AC: 33AN: 140824Hom.: 0 AF XY: 0.000199 AC XY: 15AN XY: 75438
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GnomAD4 exome AF: 0.0000921 AC: 128AN: 1389362Hom.: 0 AF XY: 0.0000846 AC XY: 58AN XY: 685404
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GnomAD4 genome ? AF: 0.000172 AC: 26AN: 151524Hom.: 0 Cov.: 31 AF XY: 0.000243 AC XY: 18AN XY: 74000
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ClinVar
Significance: Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 15, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 03, 2023 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 17, 2015 | - - |
ARID1B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 03, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 23, 2018 | This alteration is classified as likely 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. - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at