rs12685
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006015.6(ARID1A):c.*998T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.058 in 233,710 control chromosomes in the GnomAD database, including 488 homozygotes. 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 0.057 ( 324 hom., cov: 32)
Exomes 𝑓: 0.059 ( 164 hom. )
Consequence
ARID1A
NM_006015.6 3_prime_UTR
NM_006015.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.51
Genes affected
ARID1A (HGNC:11110): (AT-rich interaction domain 1A) This gene encodes a member of the SWI/SNF family, whose members have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. It possesses at least two conserved domains that could be important for its function. First, it has a DNA-binding domain that can specifically bind an AT-rich DNA sequence known to be recognized by a SNF/SWI complex at the beta-globin locus. Second, the C-terminus of the protein can stimulate glucocorticoid receptor-dependent transcriptional activation. It is thought that the protein encoded by this gene confers specificity to the SNF/SWI complex and may recruit the complex to its targets through either protein-DNA or protein-protein interactions. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0781 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1A | NM_006015.6 | c.*998T>C | 3_prime_UTR_variant | 20/20 | ENST00000324856.13 | ||
ARID1A | NM_139135.4 | c.*998T>C | 3_prime_UTR_variant | 20/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1A | ENST00000324856.13 | c.*998T>C | 3_prime_UTR_variant | 20/20 | 1 | NM_006015.6 | |||
ARID1A | ENST00000636219.1 | c.*998T>C | 3_prime_UTR_variant | 19/19 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0574 AC: 8734AN: 152210Hom.: 323 Cov.: 32
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GnomAD4 exome AF: 0.0590 AC: 4804AN: 81382Hom.: 164 Cov.: 0 AF XY: 0.0588 AC XY: 2204AN XY: 37460
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GnomAD4 genome ? AF: 0.0574 AC: 8741AN: 152328Hom.: 324 Cov.: 32 AF XY: 0.0570 AC XY: 4248AN XY: 74482
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at