10-62070527-T-C

Position:

• chr10-62070527-T-C

Variant summary

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

The ENST00000279873.12(ARID5B):​c.1199+730T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,124 control chromosomes in the GnomAD database, including 9,005 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 0.33 (9005 hom., cov: 32)
• Consequence: ARID5B ENST00000279873.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.1199+730T>C		intron_variant		ENST00000279873.12	NP_115575.1
ARID5B	NM_001244638.2	c.470+730T>C		intron_variant			NP_001231567.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARID5B	ENST00000279873.12	c.1199+730T>C		intron_variant		1	NM_032199.3	ENSP00000279873	P3
ARID5B	ENST00000309334.5	c.470+730T>C		intron_variant		5		ENSP00000308862	A1
ARID5B	ENST00000681100.1	c.1175+730T>C		intron_variant				ENSP00000506119

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50172 AN: 152006 Hom.: 9011 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.330 AC: 50158 AN: 152124 Hom.: 9005 Cov.: 32 AF XY: 0.328 AC XY: 24370 AN XY: 74352

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.309

Alfa AF: 0.380 Hom.: 5375

Bravo AF: 0.315

Asia WGS AF: 0.335 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	12
DANN	Benign	0.71

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: rs7090871; hg19: chr10-63830286;