rs10994983

chr10-61953068-G-C

Variant summary

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

The NM_032199.3(ARID5B):c.502+12660G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0644 in 151,780 control chromosomes in the GnomAD database, including 406 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 0.064 (406 hom., cov: 32)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

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=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID5B	NM_032199.3	c.502+12660G>C		intron_variant		ENST00000279873.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID5B	ENST00000279873.12	c.502+12660G>C		intron_variant		1	NM_032199.3	P3
ARID5B	ENST00000644638.1	c.502+12660G>C		intron_variant
ARID5B	ENST00000681100.1	c.502+12660G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9778 AN: 151664 Hom.: 406 Cov.: 32

Gnomad AFR AF: 0.0285

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0441

Gnomad ASJ AF: 0.0969

Gnomad EAS AF: 0.0322

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0644 AC: 9777 AN: 151780 Hom.: 406 Cov.: 32 AF XY: 0.0633 AC XY: 4694 AN XY: 74142

Gnomad4 AFR AF: 0.0284

Gnomad4 AMR AF: 0.0441

Gnomad4 ASJ AF: 0.0969

Gnomad4 EAS AF: 0.0321

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0670

Gnomad4 NFE AF: 0.0870

Gnomad4 OTH AF: 0.0672

Alfa AF: 0.0789 Hom.: 71

Bravo AF: 0.0600

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	11
Dann	Benign	0.46
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs10994983; hg19: chr10-63712827;