chr6-156778982-AGGC-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP3BP6BS1BS2
The NM_001374828.1(ARID1B):c.1318_1320delGGC(p.Gly440del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000634 in 1,261,192 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 conservative_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.1318_1320delGGC | p.Gly440del | conservative_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.1318_1320delGGC | p.Gly440del | conservative_inframe_deletion | Exon 1 of 20 | 2 | NM_001374828.1 | ENSP00000490491.2 |
Frequencies
GnomAD3 genomes AF: 0.00184 AC: 252AN: 137288Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.00159 AC: 3AN: 1892Hom.: 0 AF XY: 0.00175 AC XY: 2AN XY: 1144
GnomAD4 exome AF: 0.000485 AC: 545AN: 1123798Hom.: 1 AF XY: 0.000486 AC XY: 263AN XY: 541002
GnomAD4 genome AF: 0.00185 AC: 254AN: 137394Hom.: 0 Cov.: 29 AF XY: 0.00169 AC XY: 114AN XY: 67284
ClinVar
Submissions by phenotype
not provided Benign:4
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not specified Uncertain:1Benign:1
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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