GeneBe

rs587779743

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP3BP6_ModerateBS2_Supporting

The NM_001374828.1(ARID1B):​c.591_611delGCAGCAGCAGCAGCAGCAGCA​(p.Gln198_Gln204del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000228 in 1,536,826 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000019 ( 0 hom. )

Consequence

ARID1B
NM_001374828.1 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.90

Publications

5 publications found
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]
ARID1B Gene-Disease associations (from GenCC):
  • Coffin-Siris syndrome
    Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Illumina, ClinGen
  • Coffin-Siris syndrome 1
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001374828.1
BP6
Variant 6-156778268-CCAGCAGCAGCAGCAGCAGCAG-C is Benign according to our data. Variant chr6-156778268-CCAGCAGCAGCAGCAGCAGCAG-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2730369.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 8 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARID1BNM_001374828.1 linkc.591_611delGCAGCAGCAGCAGCAGCAGCA p.Gln198_Gln204del 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.591_611delGCAGCAGCAGCAGCAGCAGCA p.Gln198_Gln204del disruptive_inframe_deletion Exon 1 of 20 2 NM_001374828.1 ENSP00000490491.2

Frequencies

GnomAD3 genomes
AF:
0.0000529
AC:
8
AN:
151256
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0000729
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000195
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000591
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000195
AC:
27
AN:
1385456
Hom.:
0
AF XY:
0.0000219
AC XY:
15
AN XY:
683558
show subpopulations
African (AFR)
AF:
0.0000319
AC:
1
AN:
31376
American (AMR)
AF:
0.00
AC:
0
AN:
35516
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25064
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35518
South Asian (SAS)
AF:
0.00
AC:
0
AN:
78742
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
41554
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5578
European-Non Finnish (NFE)
AF:
0.0000223
AC:
24
AN:
1074400
Other (OTH)
AF:
0.0000347
AC:
2
AN:
57708
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.438
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0000529
AC:
8
AN:
151370
Hom.:
0
Cov.:
30
AF XY:
0.0000811
AC XY:
6
AN XY:
73994
show subpopulations
African (AFR)
AF:
0.0000727
AC:
3
AN:
41288
American (AMR)
AF:
0.00
AC:
0
AN:
15250
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3450
East Asian (EAS)
AF:
0.000196
AC:
1
AN:
5104
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4790
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10520
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
0.0000591
AC:
4
AN:
67668
Other (OTH)
AF:
0.00
AC:
0
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.462
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
0

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 05, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.9
Mutation Taster
=77/123
disease causing (long InDel)

Splicing

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

Publications

Other links and lift over

dbSNP: rs587779743; hg19: chr6-157099402; API