6-156778283-GCAGCAGCAA-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP3BP6_Very_StrongBS2
The NM_001374828.1(ARID1B):c.612_620delACAGCAGCA(p.Gln205_Gln207del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000999 in 1,540,886 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. QQ204Q?) has been classified as Likely benign.
Frequency
Consequence
NM_001374828.1 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARID1B | NM_001374828.1 | c.612_620delACAGCAGCA | p.Gln205_Gln207del | disruptive_inframe_deletion | Exon 1 of 20 | ENST00000636930.2 | NP_001361757.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARID1B | ENST00000636930.2 | c.612_620delACAGCAGCA | p.Gln205_Gln207del | disruptive_inframe_deletion | Exon 1 of 20 | 2 | NM_001374828.1 | ENSP00000490491.2 |
Frequencies
GnomAD3 genomes AF: 0.000172 AC: 26AN: 151524Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000234 AC: 33AN: 140824Hom.: 0 AF XY: 0.000199 AC XY: 15AN XY: 75438
GnomAD4 exome AF: 0.0000921 AC: 128AN: 1389362Hom.: 0 AF XY: 0.0000846 AC XY: 58AN XY: 685404
GnomAD4 genome AF: 0.000172 AC: 26AN: 151524Hom.: 0 Cov.: 31 AF XY: 0.000243 AC XY: 18AN XY: 74000
ClinVar
Submissions by phenotype
not provided Benign:3
ARID1B: BS1 -
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not specified Benign:1
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ARID1B-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Inborn genetic diseases Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at