6-156779262-GCGCCGCCGC-GCGC

Variant names:

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP3BP6_ModerateBS2

The NM_001374828.1(ARID1B):c.1594_1599delCCGCCG(p.Pro532_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 0.0000175 in 1,146,008 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. P532P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000064 ( 0 hom., cov: 28)

Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

ARID1B
NM_001374828.1 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.88

Publications

6 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

ARID1B links:

ENSG00000296922 (HGNC:):

ENSG00000296922 links:

Genome browser will be placed here

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-GCGCCGC-G is Benign according to our data. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-156779262-GCGCCGC-G is described in CliVar as Likely_benign. Clinvar id is 2765484.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 9 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID1B	NM_001374828.1 link	c.1594_1599delCCGCCG	p.Pro532_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.1594_1599delCCGCCG	p.Pro532_Pro533del	conservative_inframe_deletion	Exon 1 of 20	2	NM_001374828.1	ENSP00000490491.2		Q8NFD5-3A0A6Q8NVI4

Frequencies

GnomAD3 genomes

AF:

0.0000643

AC:

AN:

139874

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000155

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:

0.0000475

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000616

AC:

AN:

64972

AF XY:

0.0000797

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000110

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000109

AC:

AN:

1006134

Hom.:

AF XY:

0.0000104

AC XY:

AN XY:

480482

show subpopulations

African (AFR)

AF:

0.0000493

AC:

AN:

20280

American (AMR)

AF:

0.00

AC:

AN:

12724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10068

East Asian (EAS)

AF:

0.00

AC:

AN:

19772

South Asian (SAS)

AF:

0.00

AC:

AN:

24952

European-Finnish (FIN)

AF:

0.00

AC:

AN:

13254

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2664

European-Non Finnish (NFE)

AF:

0.0000115

AC:

AN:

866172

Other (OTH)

AF:

0.00

AC:

AN:

36248

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.552

Heterozygous variant carriers

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:

0.0000643

AC:

AN:

139874

Hom.:

Cov.:

AF XY:

0.0000441

AC XY:

AN XY:

68024

show subpopulations

African (AFR)

AF:

0.000155

AC:

AN:

38714

American (AMR)

AF:

0.00

AC:

AN:

14488

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:

0.0000475

AC:

AN:

63224

Other (OTH)

AF:

0.00

AC:

AN:

1928

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

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

Alfa

AF:

0.00

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Oct 16, 2024

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

2.9

Mutation Taster

=169/31

polymorphism

(source)

Splicing

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