rs10994993

chr10-61978324-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.503-21767A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,060 control chromosomes in the GnomAD database, including 1,164 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 0.11 (1164 hom., cov: 32)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID5B	NM_032199.3	c.503-21767A>G		intron_variant		ENST00000279873.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID5B	ENST00000279873.12	c.503-21767A>G		intron_variant		1	NM_032199.3	P3
ARID5B	ENST00000644638.1	c.503-21767A>G		intron_variant
ARID5B	ENST00000681100.1	c.503-21767A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17119 AN: 151942 Hom.: 1159 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.0315

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0669

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.113 AC: 17147 AN: 152060 Hom.: 1164 Cov.: 32 AF XY: 0.110 AC XY: 8182 AN XY: 74346

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.0631

Gnomad4 ASJ AF: 0.0975

Gnomad4 EAS AF: 0.0314

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0669

Gnomad4 NFE AF: 0.0861

Gnomad4 OTH AF: 0.104

Alfa AF: 0.106 Hom.: 133

Bravo AF: 0.116

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.43
Dann	Benign	0.23

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: rs10994993; hg19: chr10-63738083;