rs1015322780
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_006015.6(ARID1A):c.255_260del(p.Gly86_Gly87del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000000864 in 1,156,858 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 8.6e-7 ( 0 hom. )
Consequence
ARID1A
NM_006015.6 inframe_deletion
NM_006015.6 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.06
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 Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_006015.6.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1A | NM_006015.6 | c.255_260del | p.Gly86_Gly87del | inframe_deletion | 1/20 | ENST00000324856.13 | |
ARID1A | NM_139135.4 | c.255_260del | p.Gly86_Gly87del | inframe_deletion | 1/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1A | ENST00000324856.13 | c.255_260del | p.Gly86_Gly87del | inframe_deletion | 1/20 | 1 | NM_006015.6 | ||
ARID1A | ENST00000457599.6 | c.255_260del | p.Gly86_Gly87del | inframe_deletion | 1/20 | 5 | |||
ARID1A | ENST00000430799.7 | c.-13+3041_-13+3046del | intron_variant | 5 | A2 | ||||
ARID1A | ENST00000637465.1 | c.-13+558_-13+563del | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 8.64e-7 AC: 1AN: 1156858Hom.: 0 AF XY: 0.00000178 AC XY: 1AN XY: 561126
GnomAD4 exome
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1
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1156858
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1
AN XY:
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.