rs797045274

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

Genomes: 𝑓 0.00017 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000092 ( 0 hom. )

Consequence

ARID1B
NM_001374828.1 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 3.85
Variant links:
Genes affected
ARID1B (HGNC:18040): (AT-rich interaction domain 1B) This locus encodes an AT-rich DNA interacting domain-containing protein. The encoded protein is a component of the SWI/SNF chromatin remodeling complex and may play a role in cell-cycle activation. The protein encoded by this locus is similar to AT-rich interactive domain-containing protein 1A. These two proteins function as alternative, mutually exclusive ARID-subunits of the SWI/SNF complex. The associated complexes play opposing roles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001374828.1
BP6
Variant 6-156778283-GCAGCAGCAA-G is Benign according to our data. Variant chr6-156778283-GCAGCAGCAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 210285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-156778283-GCAGCAGCAA-G is described in Lovd as [Likely_benign].
BS2
High AC in GnomAd4 at 26 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARID1BNM_001374828.1 linkc.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
ARID1BENST00000636930.2 linkc.612_620delACAGCAGCA p.Gln205_Gln207del disruptive_inframe_deletion Exon 1 of 20 2 NM_001374828.1 ENSP00000490491.2 Q8NFD5-3A0A6Q8NVI4

Frequencies

GnomAD3 genomes
AF:
0.000172
AC:
26
AN:
151524
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000145
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000656
Gnomad ASJ
AF:
0.00405
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000738
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000234
AC:
33
AN:
140824
Hom.:
0
AF XY:
0.000199
AC XY:
15
AN XY:
75438
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00339
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000886
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000386
Gnomad OTH exome
AF:
0.000239
GnomAD4 exome
AF:
0.0000921
AC:
128
AN:
1389362
Hom.:
0
AF XY:
0.0000846
AC XY:
58
AN XY:
685404
show subpopulations
Gnomad4 AFR exome
AF:
0.0000636
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00323
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000380
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000232
Gnomad4 OTH exome
AF:
0.000294
GnomAD4 genome
AF:
0.000172
AC:
26
AN:
151524
Hom.:
0
Cov.:
31
AF XY:
0.000243
AC XY:
18
AN XY:
74000
show subpopulations
Gnomad4 AFR
AF:
0.000145
Gnomad4 AMR
AF:
0.0000656
Gnomad4 ASJ
AF:
0.00405
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000738
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2024ARID1B: BS1 -
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 31, 2024- -
Likely benign, criteria provided, single submitterclinical testingGeneDxDec 15, 2020- -
not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoMar 17, 2015- -
ARID1B-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesMay 03, 2022This 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
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsMar 23, 2018This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs797045274; hg19: chr6-157099417; API