10-61925395-C-T

Position:

• chr10-61925395-C-T

Variant summary

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

The NM_032199.3(ARID5B):​c.277-14788C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 151,878 control chromosomes in the GnomAD database, including 45,819 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 0.77 (45819 hom., cov: 30)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.277-14788C>T		intron_variant		ENST00000279873.12	NP_115575.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARID5B	ENST00000279873.12	c.277-14788C>T		intron_variant		1	NM_032199.3	ENSP00000279873.7
ARID5B	ENST00000644638.1	c.277-14788C>T		intron_variant				ENSP00000494412.1
ARID5B	ENST00000681100.1	c.277-14788C>T		intron_variant				ENSP00000506119.1

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117461 AN: 151760 Hom.: 45804 Cov.: 30

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.774 AC: 117519 AN: 151878 Hom.: 45819 Cov.: 30 AF XY: 0.771 AC XY: 57200 AN XY: 74192

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.756

Alfa AF: 0.809 Hom.: 68561

Bravo AF: 0.757

Asia WGS AF: 0.724 AC: 2516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	5.2
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: rs4948488; hg19: chr10-63685154;