rs3840452

chr1-235327076-CA-Cchr1-235327076-CA-CAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_016374.6(ARID4B):c.-49-109del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 742,932 control chromosomes in the GnomAD database, including 80,178 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.45 (15802 hom., cov: 0)
  • Exomes 𝑓: 0.46 (64376 hom.)
• Consequence: ARID4B NM_016374.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

Genes affected

ARID4B (HGNC:15550): (AT-rich interaction domain 4B) This gene encodes a protein with sequence similarity to retinoblastoma-binding protein-1. The encoded protein is a subunit of the histone deacetylase-dependant SIN3A transcriptional corepressor complex, which functions in diverse cellular processes including proliferation, differentiation, apoptosis, oncogenesis, and cell fate determination. The gene product is recognized by IgG antibody isolated from a breast cancer patient and appears to be a molecular marker associated with a broad range of human malignancies. Alternate transcriptional splice variants encoding different isoforms have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID4B	NM_016374.6	c.-49-109del		intron_variant		ENST00000264183.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID4B	ENST00000264183.9	c.-49-109del		intron_variant		1	NM_016374.6	P1

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68613 AN: 151806 Hom.: 15782 Cov.: 0

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.460 AC: 271873 AN: 591008 Hom.: 64376 Cov.: 0 AF XY: 0.468 AC XY: 146220 AN XY: 312504

Gnomad4 AFR exome AF: 0.446

Gnomad4 AMR exome AF: 0.431

Gnomad4 ASJ exome AF: 0.433

Gnomad4 EAS exome AF: 0.273

Gnomad4 SAS exome AF: 0.593

Gnomad4 FIN exome AF: 0.476

Gnomad4 NFE exome AF: 0.459

Gnomad4 OTH exome AF: 0.447

GnomAD4 genome AF: 0.452 AC: 68668 AN: 151924 Hom.: 15802 Cov.: 0 AF XY: 0.456 AC XY: 33832 AN XY: 74234

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.430

Alfa AF: 0.451 Hom.: 1886

Bravo AF: 0.441

Asia WGS AF: 0.422 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs3840452; hg19: chr1-235490391;