chr6-156778889-CGGAGGA-C

Variant names:

• chr6-156778889-CGGAGGA-C
• rs747790383
• NM_001374828.1:c.1229_1234delGAGGAG

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP3 BP6_Very_Strong BS1 BS2

The NM_001374828.1(ARID1B):​c.1229_1234delGAGGAG​(p.Gly410_Gly411del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00201 in 1,366,178 control chromosomes in the GnomAD database, including 14 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0034 (2 hom., cov: 29)
  • Exomes 𝑓: 0.0018 (12 hom.)
• Consequence: ARID1B NM_001374828.1 disruptive_inframe_deletion
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6
• Conservation: PhyloP100: 3.18

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]

ACMG classification

Verdict is Benign. Variant got -17 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001374828.1
• BP6: Variant 6-156778889-CGGAGGA-C is Benign according to our data. Variant chr6-156778889-CGGAGGA-C is described in ClinVar as [Likely_benign]. Clinvar id is 434354.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0034 (486/143050) while in subpopulation AMR AF= 0.00522 (76/14550). AF 95% confidence interval is 0.00428. There are 2 homozygotes in gnomad4. There are 315 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 486 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID1B	NM_001374828.1	c.1229_1234delGAGGAG	p.Gly410_Gly411del	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
ARID1B	ENST00000636930.2	c.1229_1234delGAGGAG	p.Gly410_Gly411del	disruptive_inframe_deletion	Exon 1 of 20	2	NM_001374828.1	ENSP00000490491.2

Frequencies

GnomAD3 genomes AF: 0.00339 AC: 485 AN: 142976 Hom.: 2 Cov.: 29

Gnomad AFR AF: 0.00296

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00523

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00255

Gnomad SAS AF: 0.00448

Gnomad FIN AF: 0.0187

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00134

Gnomad OTH AF: 0.00102

GnomAD3 exomes AF: 0.00465 AC: 155 AN: 33354 Hom.: 3 AF XY: 0.00439 AC XY: 87 AN XY: 19836

Gnomad AFR exome AF: 0.00347

Gnomad AMR exome AF: 0.00115

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00178

Gnomad FIN exome AF: 0.0143

Gnomad NFE exome AF: 0.00104

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00185 AC: 2260 AN: 1223128 Hom.: 12 AF XY: 0.00184 AC XY: 1100 AN XY: 599130

Gnomad4 AFR exome AF: 0.00255

Gnomad4 AMR exome AF: 0.00192

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00418

Gnomad4 SAS exome AF: 0.00283

Gnomad4 FIN exome AF: 0.0149

Gnomad4 NFE exome AF: 0.00123

Gnomad4 OTH exome AF: 0.00170

GnomAD4 genome AF: 0.00340 AC: 486 AN: 143050 Hom.: 2 Cov.: 29 AF XY: 0.00451 AC XY: 315 AN XY: 69788

Gnomad4 AFR AF: 0.00301

Gnomad4 AMR AF: 0.00522

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00256

Gnomad4 SAS AF: 0.00450

Gnomad4 FIN AF: 0.0187

Gnomad4 NFE AF: 0.00133

Gnomad4 OTH AF: 0.00101

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

Sep 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ARID1B: BS1, BS2 -

Oct 09, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Benign:1

Jul 22, 2016

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

ARID1B-related disorder Benign:1

Mar 27, 2024

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Inborn genetic diseases Benign:1

May 16, 2017

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs747790383; hg19: chr6-157100023;