NM_001374828.1:c.1591_1599delCCGCCGCCG
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP3BP6_ModerateBS2
The NM_001374828.1(ARID1B):c.1591_1599delCCGCCGCCG(p.Pro531_Pro533del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000895 in 1,006,140 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. P531P) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 28)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
ARID1B
NM_001374828.1 conservative_inframe_deletion
NM_001374828.1 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.88
Publications
6 publications found
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 syndromeInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Illumina, ClinGen
- Coffin-Siris syndrome 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -7 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001374828.1
BP6
Variant 6-156779262-GCGCCGCCGC-G is Benign according to our data. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2170599.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 9 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ARID1B | NM_001374828.1 | c.1591_1599delCCGCCGCCG | p.Pro531_Pro533del | 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.1591_1599delCCGCCGCCG | p.Pro531_Pro533del | conservative_inframe_deletion | Exon 1 of 20 | 2 | NM_001374828.1 | ENSP00000490491.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
28
GnomAD4 exome AF: 0.00000895 AC: 9AN: 1006140Hom.: 0 AF XY: 0.00000832 AC XY: 4AN XY: 480486 show subpopulations
GnomAD4 exome
AF:
AC:
9
AN:
1006140
Hom.:
AF XY:
AC XY:
4
AN XY:
480486
show subpopulations
African (AFR)
AF:
AC:
0
AN:
20280
American (AMR)
AF:
AC:
1
AN:
12724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
10068
East Asian (EAS)
AF:
AC:
0
AN:
19772
South Asian (SAS)
AF:
AC:
0
AN:
24952
European-Finnish (FIN)
AF:
AC:
0
AN:
13256
Middle Eastern (MID)
AF:
AC:
0
AN:
2664
European-Non Finnish (NFE)
AF:
AC:
8
AN:
866174
Other (OTH)
AF:
AC:
0
AN:
36250
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.547
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
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
GnomAD4 genome
Cov.:
28
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Sep 01, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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