rs4506592

Positions:

• chr10-61967428-A-G

Variant summary

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

The NM_032199.3(ARID5B):​c.502+27020A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,120 control chromosomes in the GnomAD database, including 32,426 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 0.65 (32426 hom., cov: 33)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768

Genes affected

ARID5B (HGNC:17362): (AT-rich interaction domain 5B) This gene encodes a member of the AT-rich interaction domain (ARID) family of DNA binding proteins. The encoded protein forms a histone H3K9Me2 demethylase complex with PHD finger protein 2 and regulates the transcription of target genes involved in adipogenesis and liver development. This gene also plays a role in cell growth and differentiation of B-lymphocyte progenitors, and single nucleotide polymorphisms in this gene are associated with acute lymphoblastic leukemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID5B	NM_032199.3	c.502+27020A>G		intron_variant		ENST00000279873.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID5B	ENST00000279873.12	c.502+27020A>G		intron_variant		1	NM_032199.3	P3
ARID5B	ENST00000644638.1	c.502+27020A>G		intron_variant
ARID5B	ENST00000681100.1	c.502+27020A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98813 AN: 152002 Hom.: 32404 Cov.: 33

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.650 AC: 98878 AN: 152120 Hom.: 32426 Cov.: 33 AF XY: 0.648 AC XY: 48198 AN XY: 74344

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.629

Alfa AF: 0.639 Hom.: 30271

Bravo AF: 0.639

Asia WGS AF: 0.640 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	4.3
DANN	Benign	0.73

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: rs4506592; hg19: chr10-63727187;