6-156779262-GCGCCGCCGC-GCGCCGC

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP3BP6

The NM_001374828.1(ARID1B):c.1597_1599delCCG(p.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 0.000119 in 1,145,108 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0000071 ( 0 hom., cov: 28)

Exomes 𝑓: 0.00013 ( 0 hom. )

Consequence

ARID1B
NM_001374828.1 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.81

Publications

6 publications found

Variant links:

COSMIC-nc: COSV105108030

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

ARID1B links:

ENSG00000296922 (HGNC:):

ENSG00000296922 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001374828.1

BP6

Variant 6-156779262-GCGC-G is Benign according to our data. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-156779262-GCGC-G is described in CliVar as Likely_benign. Clinvar id is 3353308.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID1B	NM_001374828.1 link	c.1597_1599delCCG	p.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 link	c.1597_1599delCCG	p.Pro533del	conservative_inframe_deletion	Exon 1 of 20	2	NM_001374828.1	ENSP00000490491.2		Q8NFD5-3A0A6Q8NVI4

Frequencies

GnomAD3 genomes

AF:

0.00000715

AC:

AN:

139872

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000158

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000169

AC:

AN:

64972

AF XY:

0.000133

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000254

Gnomad ASJ exome

AF:

0.000799

Gnomad EAS exome

AF:

0.000547

Gnomad FIN exome

AF:

0.000359

Gnomad NFE exome

AF:

0.000110

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000134

AC:

135

AN:

1005236

Hom.:

AF XY:

0.000163

AC XY:

AN XY:

479950

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000197

AC:

AN:

20260

American (AMR)

AF:

0.000630

AC:

AN:

12700

Ashkenazi Jewish (ASJ)

AF:

0.000199

AC:

AN:

10038

East Asian (EAS)

AF:

0.000456

AC:

AN:

19720

South Asian (SAS)

AF:

0.0000802

AC:

AN:

24932

European-Finnish (FIN)

AF:

0.00106

AC:

AN:

13194

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2658

European-Non Finnish (NFE)

AF:

0.000101

AC:

AN:

865532

Other (OTH)

AF:

0.000249

AC:

AN:

36202

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.243

Heterozygous variant carriers

113

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.00000715

AC:

AN:

139872

Hom.:

Cov.:

AF XY:

0.0000147

AC XY:

AN XY:

68024

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

38714

American (AMR)

AF:

0.00

AC:

AN:

14486

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3318

East Asian (EAS)

AF:

0.00

AC:

AN:

4518

South Asian (SAS)

AF:

0.00

AC:

AN:

4532

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8070

Middle Eastern (MID)

AF:

0.00

AC:

AN:

252

European-Non Finnish (NFE)

AF:

0.0000158

AC:

AN:

63224

Other (OTH)

AF:

0.00

AC:

AN:

1928

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.225

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ARID1B-related disorder

Benign:1

Jul 03, 2024

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This 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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.8

Mutation Taster

=82/18

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over