rs587779743
Positions:
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-C
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP3BP6_ModerateBS2_Supporting
The NM_001374828.1(ARID1B):c.591_611delGCAGCAGCAGCAGCAGCAGCA(p.Gln198_Gln204del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000228 in 1,536,826 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
ARID1B
NM_001374828.1 disruptive_inframe_deletion
NM_001374828.1 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.90
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 -4 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001374828.1
BP6
Variant 6-156778268-CCAGCAGCAGCAGCAGCAGCAG-C is Benign according to our data. Variant chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-C is described in ClinVar as [Likely_benign]. Clinvar id is 2730369.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 8 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ARID1B | NM_001374828.1 | c.591_611delGCAGCAGCAGCAGCAGCAGCA | p.Gln198_Gln204del | 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.591_611delGCAGCAGCAGCAGCAGCAGCA | p.Gln198_Gln204del | disruptive_inframe_deletion | 1/20 | 2 | NM_001374828.1 | ENSP00000490491.2 |
Frequencies
GnomAD3 genomes 0.0000529 AC: 8AN: 151256Hom.: 0 Cov.: 30
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GnomAD4 exome AF: 0.0000195 AC: 27AN: 1385456Hom.: 0 AF XY: 0.0000219 AC XY: 15AN XY: 683558
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GnomAD4 genome 0.0000529 AC: 8AN: 151370Hom.: 0 Cov.: 30 AF XY: 0.0000811 AC XY: 6AN XY: 73994
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 05, 2023 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at