rs754242891
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001374828.1(ARID1B):c.6963G>A(p.Ala2321=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000901 in 1,587,572 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000092 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000090 ( 1 hom. )
Consequence
ARID1B
NM_001374828.1 synonymous
NM_001374828.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.717
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 6-157207735-G-A is Benign according to our data. Variant chr6-157207735-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 210308.We mark this variant Likely_benign, oryginal submissions are: {Benign=3, Uncertain_significance=1, Likely_benign=2}.
BP7
Synonymous conserved (PhyloP=-0.717 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0000899 (129/1435462) while in subpopulation AMR AF= 0.00127 (55/43274). AF 95% confidence interval is 0.001. There are 1 homozygotes in gnomad4_exome. There are 52 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARID1B | NM_001374828.1 | c.6963G>A | p.Ala2321= | synonymous_variant | 20/20 | ENST00000636930.2 | NP_001361757.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARID1B | ENST00000636930.2 | c.6963G>A | p.Ala2321= | synonymous_variant | 20/20 | 2 | NM_001374828.1 | ENSP00000490491 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152110Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000246 AC: 60AN: 243492Hom.: 0 AF XY: 0.000175 AC XY: 23AN XY: 131478
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GnomAD4 exome AF: 0.0000899 AC: 129AN: 1435462Hom.: 1 Cov.: 31 AF XY: 0.0000734 AC XY: 52AN XY: 708690
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GnomAD4 genome AF: 0.0000920 AC: 14AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74288
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:5
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 09, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | ARID1B: BS1, BS2 - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 10, 2015 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2017 | 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. - |
Coffin-Siris syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at