rs587779747
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr6-156778847-GGGCGGCGGCGGCGGCGGC-G
- chr6-156778847-GGGCGGCGGCGGCGGCGGC-GGGC
- chr6-156778847-GGGCGGCGGCGGCGGCGGC-GGGCGGC
- chr6-156778847-GGGCGGCGGCGGCGGCGGC-GGGCGGCGGC
- chr6-156778847-GGGCGGCGGCGGCGGCGGC-GGGCGGCGGCGGC
- chr6-156778847-GGGCGGCGGCGGCGGCGGC-GGGCGGCGGCGGCGGC
- chr6-156778847-GGGCGGCGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGC
- chr6-156778847-GGGCGGCGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGC
- chr6-156778847-GGGCGGCGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGCGGC
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_001374828.1(ARID1B):c.1176_1193delCGGCGGCGGCGGCGGCGG(p.Gly393_Gly398del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000214 in 1,403,412 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000068 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0000016 ( 0 hom. )
Consequence
ARID1B
NM_001374828.1 disruptive_inframe_deletion
NM_001374828.1 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.68
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 Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_001374828.1
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ARID1B | NM_001374828.1 | c.1176_1193delCGGCGGCGGCGGCGGCGG | p.Gly393_Gly398del | disruptive_inframe_deletion | Exon 1 of 20 | ENST00000636930.2 | NP_001361757.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ARID1B | ENST00000636930.2 | c.1176_1193delCGGCGGCGGCGGCGGCGG | p.Gly393_Gly398del | disruptive_inframe_deletion | Exon 1 of 20 | 2 | NM_001374828.1 | ENSP00000490491.2 |
Frequencies
GnomAD3 genomes 0.00000676 AC: 1AN: 147820Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 0.00000159 AC: 2AN: 1255592Hom.: 0 AF XY: 0.00000324 AC XY: 2AN XY: 617180
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GnomAD4 genome 0.00000676 AC: 1AN: 147820Hom.: 0 Cov.: 29 AF XY: 0.0000139 AC XY: 1AN XY: 72166
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Oct 22, 2024 | This variant, c.927_944del, results in the deletion of 6 amino acid(s) of the ARID1B protein (p.Gly314_Gly319del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). 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