Variant 6-156777818-C-CGCG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBS1BS2

The NM_001374828.1(ARID1B):c.156_158dup(p.Ala52dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 1,011,732 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0019 ( 1 hom., cov: 30)

Exomes 𝑓: 0.0013 ( 1 hom. )

Consequence

ARID1B
NM_001374828.1 inframe_insertion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.490

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 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001374828.1

BP6

Variant 6-156777818-C-CGCG is Benign according to our data. Variant chr6-156777818-C-CGCG is described in ClinVar as [Likely_benign]. Clinvar id is 2579011.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00186 (264/142248) while in subpopulation AFR AF= 0.00278 (110/39498). AF 95% confidence interval is 0.00236. There are 1 homozygotes in gnomad4. There are 125 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High AC in GnomAd4 at 264 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID1B	NM_001374828.1 linkuse as main transcript	c.156_158dup	p.Ala52dup	inframe_insertion	1/20	ENST00000636930.2
LOC115308161	NR_163974.1 linkuse as main transcript	n.274-388_274-387insCGC		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID1B	ENST00000636930.2 linkuse as main transcript	c.156_158dup	p.Ala52dup	inframe_insertion	1/20	2	NM_001374828.1	A2	Q8NFD5-3
	ENST00000603191.2 linkuse as main transcript	n.178-388_178-387insCGC		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00185

AC:

263

AN:

142230

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00276

Gnomad AMI

AF:

0.00917

Gnomad AMR

AF:

0.00110

Gnomad ASJ

AF:

0.000298

Gnomad EAS

AF:

0.00166

Gnomad SAS

AF:

0.00258

Gnomad FIN

AF:

0.000375

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00160

Gnomad OTH

AF:

0.00154

GnomAD4 exome

AF:

0.00131

AC:

1140

AN:

869484

Hom.:

Cov.:

AF XY:

0.00129

AC XY:

522

AN XY:

404808

show subpopulations

Gnomad4 AFR exome

AF:

0.00177

Gnomad4 AMR exome

AF:

0.000869

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00100

Gnomad4 SAS exome

AF:

0.00285

Gnomad4 FIN exome

AF:

0.000216

Gnomad4 NFE exome

AF:

0.00130

Gnomad4 OTH exome

AF:

0.00114

GnomAD4 genome

AF:

0.00186

AC:

264

AN:

142248

Hom.:

Cov.:

AF XY:

0.00181

AC XY:

125

AN XY:

69172

show subpopulations

Gnomad4 AFR

AF:

0.00278

Gnomad4 AMR

AF:

0.00110

Gnomad4 ASJ

AF:

0.000298

Gnomad4 EAS

AF:

0.00166

Gnomad4 SAS

AF:

0.00259

Gnomad4 FIN

AF:

0.000375

Gnomad4 NFE

AF:

0.00160

Gnomad4 OTH

AF:

0.00152

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2024

ARID1B: BS1 -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over