6-156778847-GGGCGGCGGCGGCGGCGGC-GGGCGGC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP3BP6BS1BS2
The NM_001374828.1(ARID1B):c.1182_1193delCGGCGGCGGCGG(p.Gly395_Gly398del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000912 in 1,403,380 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001374828.1 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARID1B | NM_001374828.1 | c.1182_1193delCGGCGGCGGCGG | p.Gly395_Gly398del | 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.1182_1193delCGGCGGCGGCGG | p.Gly395_Gly398del | disruptive_inframe_deletion | Exon 1 of 20 | 2 | NM_001374828.1 | ENSP00000490491.2 |
Frequencies
GnomAD3 genomes AF: 0.0000947 AC: 14AN: 147822Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000540 AC: 3AN: 55508Hom.: 0 AF XY: 0.0000609 AC XY: 2AN XY: 32826
GnomAD4 exome AF: 0.0000908 AC: 114AN: 1255558Hom.: 1 AF XY: 0.0000891 AC XY: 55AN XY: 617162
GnomAD4 genome AF: 0.0000947 AC: 14AN: 147822Hom.: 0 Cov.: 29 AF XY: 0.0000970 AC XY: 7AN XY: 72166
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
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ARID1B: BP3, BS2 -
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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