chr6-156777818-C-CGCG
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBS1BS2
The NM_001374828.1(ARID1B):c.156_158dup(p.Ala52dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 1,011,732 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 1 hom., cov: 30)
Exomes 𝑓: 0.0013 ( 1 hom. )
Consequence
ARID1B
NM_001374828.1 inframe_insertion
NM_001374828.1 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.490
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 -11 ACMG points.
BP3
?
Nonframeshift variant in repetitive region in NM_001374828.1
BP6
?
Variant 6-156777818-C-CGCG is Benign according to our data. Variant chr6-156777818-C-CGCG is described in ClinVar as [Likely_benign]. Clinvar id is 2579011.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00186 (264/142248) while in subpopulation AFR AF= 0.00278 (110/39498). AF 95% confidence interval is 0.00236. There are 1 homozygotes in gnomad4. There are 125 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High AC in GnomAd at 263 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1B | NM_001374828.1 | c.156_158dup | p.Ala52dup | inframe_insertion | 1/20 | ENST00000636930.2 | |
LOC115308161 | NR_163974.1 | n.274-388_274-387insCGC | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1B | ENST00000636930.2 | c.156_158dup | p.Ala52dup | inframe_insertion | 1/20 | 2 | NM_001374828.1 | A2 | |
ENST00000603191.2 | n.178-388_178-387insCGC | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00185 AC: 263AN: 142230Hom.: 1 Cov.: 30
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GnomAD4 exome AF: 0.00131 AC: 1140AN: 869484Hom.: 1 Cov.: 18 AF XY: 0.00129 AC XY: 522AN XY: 404808
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GnomAD4 genome ? AF: 0.00186 AC: 264AN: 142248Hom.: 1 Cov.: 30 AF XY: 0.00181 AC XY: 125AN XY: 69172
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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 | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | ARID1B: BS1 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at