12-45855644-T-C

Variant summary

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

The NM_152641.4(ARID2):c.4773+2748T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 152,126 control chromosomes in the GnomAD database, including 31,020 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 0.62 (31020 hom., cov: 32)
• Consequence: ARID2 NM_152641.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

ARID2 (HGNC:18037): (AT-rich interaction domain 2) This gene encodes a member of the AT-rich interactive domain (ARID)-containing family of DNA-binding proteins. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and chromatin structure modification. This protein functions as a subunit of the polybromo- and BRG1-associated factor or PBAF (SWI/SNF-B) chromatin remodeling complex which facilitates ligand-dependent transcriptional activation by nuclear receptors. Mutations in this gene are associated with hepatocellular carcinomas. A pseudogene of this gene is found on chromosome1. [provided by RefSeq, Dec 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID2	NM_152641.4	c.4773+2748T>C		intron_variant		ENST00000334344.11
ARID2	NM_001347839.2	c.4773+2748T>C		intron_variant
ARID2	XM_047428489.1	c.4831+1407T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID2	ENST00000334344.11	c.4773+2748T>C		intron_variant		1	NM_152641.4	P1

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93815 AN: 152008 Hom.: 30964 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.617 AC: 93913 AN: 152126 Hom.: 31020 Cov.: 32 AF XY: 0.613 AC XY: 45581 AN XY: 74362

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.599

Alfa AF: 0.592 Hom.: 4095

Bravo AF: 0.637

Asia WGS AF: 0.536 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.4
Dann	Benign	0.59

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: rs35115; hg19: chr12-46249427;