6-157196311-C-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BP7
The NM_001374828.1(ARID1B):c.4378C>A(p.Arg1460=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000126 in 1,585,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 7.0e-7 ( 0 hom. )
Consequence
ARID1B
NM_001374828.1 synonymous
NM_001374828.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.91
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 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.12).
BP7
Synonymous conserved (PhyloP=1.91 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ARID1B | NM_001374828.1 | c.4378C>A | p.Arg1460= | synonymous_variant | 16/20 | ENST00000636930.2 | NP_001361757.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ARID1B | ENST00000636930.2 | c.4378C>A | p.Arg1460= | synonymous_variant | 16/20 | 2 | NM_001374828.1 | ENSP00000490491 | A2 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000900 AC: 2AN: 222208Hom.: 0 AF XY: 0.0000166 AC XY: 2AN XY: 120732
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GnomAD4 exome AF: 6.98e-7 AC: 1AN: 1432978Hom.: 0 Cov.: 30 AF XY: 0.00000140 AC XY: 1AN XY: 712728
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GnomAD4 genome 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74292
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Not reported inComputational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at