rs9415636

chr10-62066427-G-T

Variant summary

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

The NM_032199.3(ARID5B):c.1102-3273G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.059 in 152,212 control chromosomes in the GnomAD database, including 374 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 0.059 (374 hom., cov: 32)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID5B	NM_032199.3	c.1102-3273G>T		intron_variant		ENST00000279873.12
ARID5B	NM_001244638.2	c.373-3273G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID5B	ENST00000279873.12	c.1102-3273G>T		intron_variant		1	NM_032199.3	P3
ARID5B	ENST00000309334.5	c.373-3273G>T		intron_variant		5		A1
ARID5B	ENST00000681100.1	c.1078-3273G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0591 AC: 8995 AN: 152094 Hom.: 375 Cov.: 32

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0564

Gnomad ASJ AF: 0.0736

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0914

Gnomad OTH AF: 0.0855

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

GnomAD4 genome AF: 0.0590 AC: 8988 AN: 152212 Hom.: 374 Cov.: 32 AF XY: 0.0569 AC XY: 4231 AN XY: 74416

Gnomad4 AFR AF: 0.0157

Gnomad4 AMR AF: 0.0562

Gnomad4 ASJ AF: 0.0736

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0299

Gnomad4 FIN AF: 0.0512

Gnomad4 NFE AF: 0.0914

Gnomad4 OTH AF: 0.0846

Alfa AF: 0.0774 Hom.: 289

Bravo AF: 0.0577

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.5
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9415636; hg19: chr10-63826186;