6-157167056-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001374828.1(ARID1B):c.3106G>A(p.Gly1036Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000993 in 1,611,808 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1036R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001374828.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1B | NM_001374828.1 | c.3106G>A | p.Gly1036Ser | missense_variant | 9/20 | ENST00000636930.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1B | ENST00000636930.2 | c.3106G>A | p.Gly1036Ser | missense_variant | 9/20 | 2 | NM_001374828.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00551 AC: 839AN: 152184Hom.: 7 Cov.: 33
GnomAD3 exomes AF: 0.00147 AC: 366AN: 249620Hom.: 3 AF XY: 0.00114 AC XY: 154AN XY: 135046
GnomAD4 exome AF: 0.000521 AC: 761AN: 1459506Hom.: 1 Cov.: 30 AF XY: 0.000432 AC XY: 314AN XY: 726186
GnomAD4 genome AF: 0.00551 AC: 839AN: 152302Hom.: 7 Cov.: 33 AF XY: 0.00508 AC XY: 378AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 02, 2022 | See Variant Classification Assertion Criteria. - |
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 14, 2017 | - - |
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2017 | This alteration is classified as 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. - |
Coffin-Siris syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at