rs9478751

Positions:

• chr6-157119916-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001374828.1(ARID1B):​c.2581+9355A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,120 control chromosomes in the GnomAD database, including 9,355 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (9355 hom., cov: 33)
• Consequence: ARID1B NM_001374828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID1B	NM_001374828.1	c.2581+9355A>G		intron_variant		ENST00000636930.2	NP_001361757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARID1B	ENST00000636930.2	c.2581+9355A>G		intron_variant		2	NM_001374828.1	ENSP00000490491.2

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44810 AN: 152002 Hom.: 9335 Cov.: 33

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0142

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.262

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.295 AC: 44878 AN: 152120 Hom.: 9355 Cov.: 33 AF XY: 0.286 AC XY: 21289 AN XY: 74382

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.261

Alfa AF: 0.204 Hom.: 2724

Bravo AF: 0.311

Asia WGS AF: 0.114 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.5
DANN	Benign	0.88

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

LitVar

Other links and lift over

dbSNP: rs9478751; hg19: chr6-157441050; COSMIC: COSV51655596; COSMIC: COSV51655596;