rs10821944

Positions:

• chr10-62025330-G-T

Variant summary

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

The ENST00000644638.1(ARID5B):​c.*626G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,026 control chromosomes in the GnomAD database, including 33,858 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 0.66 (33858 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ARID5B ENST00000644638.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.733+25009G>T		intron_variant		ENST00000279873.12	NP_115575.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARID5B	ENST00000644638.1	c.*626G>T		3_prime_UTR_variant	5/5			ENSP00000494412.1
ARID5B	ENST00000279873.12	c.733+25009G>T		intron_variant		1	NM_032199.3	ENSP00000279873.7
ARID5B	ENST00000681100.1	c.733+25009G>T		intron_variant				ENSP00000506119.1

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100682 AN: 151908 Hom.: 33871 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.645

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.662 AC: 100694 AN: 152026 Hom.: 33858 Cov.: 31 AF XY: 0.662 AC XY: 49196 AN XY: 74300

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.642

Alfa AF: 0.703 Hom.: 51540

Bravo AF: 0.645

Asia WGS AF: 0.612 AC: 2129 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	15
DANN	Benign	0.62

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: rs10821944; hg19: chr10-63785089;