Genetic Variant NM_001374828.1:c.4383-7A>G (chr6-157198804-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001374828.1(ARID1B):c.4383-7A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0587 in 1,604,956 control chromosomes in the GnomAD database, including 7,292 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 3167 hom., cov: 33)

Exomes 𝑓: 0.051 ( 4125 hom. )

Consequence

ARID1B
NM_001374828.1 splice_region, intron

Scores

Splicing: ADA: 0.00002729

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.414

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 6-157198804-A-G is Benign according to our data. Variant chr6-157198804-A-G is described in ClinVar as [Benign]. Clinvar id is 126330.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-157198804-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID1B	NM_001374828.1 link	c.4383-7A>G		splice_region_variant, intron_variant	Intron 16 of 19	ENST00000636930.2	NP_001361757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID1B	ENST00000636930.2 link	c.4383-7A>G		splice_region_variant, intron_variant	Intron 16 of 19	2	NM_001374828.1	ENSP00000490491.2		Q8NFD5-3A0A6Q8NVI4

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20378

AN:

152094

Hom.:

3141

Cov.:

show subpopulations

Gnomad AFR

AF:

0.380

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0774

Gnomad ASJ

AF:

0.0495

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0145

Gnomad FIN

AF:

0.0286

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0391

Gnomad OTH

AF:

0.120

GnomAD3 exomes

AF:

0.0564

AC:

13700

AN:

242846

Hom.:

1297

AF XY:

0.0476

AC XY:

6249

AN XY:

131410

show subpopulations

Gnomad AFR exome

AF:

0.386

Gnomad AMR exome

AF:

0.0553

Gnomad ASJ exome

AF:

0.0401

Gnomad EAS exome

AF:

0.000111

Gnomad SAS exome

AF:

0.0115

Gnomad FIN exome

AF:

0.0308

Gnomad NFE exome

AF:

0.0392

Gnomad OTH exome

AF:

0.0423

GnomAD4 exome

AF:

0.0507

AC:

73703

AN:

1452744

Hom.:

4125

Cov.:

AF XY:

0.0479

AC XY:

34612

AN XY:

721842

show subpopulations

Gnomad4 AFR exome

AF:

0.392

Gnomad4 AMR exome

AF:

0.0580

Gnomad4 ASJ exome

AF:

0.0431

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0125

Gnomad4 FIN exome

AF:

0.0299

Gnomad4 NFE exome

AF:

0.0456

Gnomad4 OTH exome

AF:

0.0620

GnomAD4 genome

AF:

0.134

AC:

20457

AN:

152212

Hom.:

3167

Cov.:

AF XY:

0.130

AC XY:

9714

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.381

Gnomad4 AMR

AF:

0.0778

Gnomad4 ASJ

AF:

0.0495

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0141

Gnomad4 FIN

AF:

0.0286

Gnomad4 NFE

AF:

0.0392

Gnomad4 OTH

AF:

0.120

Alfa

AF:

0.0855

Hom.:

673

Bravo

AF:

0.149

Asia WGS

AF:

0.0370

AC:

127

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 27, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Aug 15, 2013

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Coffin-Siris syndrome 1

Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.90

DANN

Benign

0.62

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000027

dbscSNV1_RF

Benign

0.0

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

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