Variant rs7073837 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032199.3(ARID5B):c.277-47A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 1,579,632 control chromosomes in the GnomAD database, including 283,708 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 0.63 ( 30714 hom., cov: 31)

Exomes 𝑓: 0.59 ( 252994 hom. )

Consequence

ARID5B
NM_032199.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.625

Variant links:

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]

ARID5B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID5B	NM_032199.3 linkuse as main transcript	c.277-47A>C		intron_variant		ENST00000279873.12	NP_115575.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
ARID5B	ENST00000279873.12 linkuse as main transcript	c.277-47A>C	intron_variant	1	NM_032199.3	ENSP00000279873	P3	Q14865-1
ARID5B	ENST00000644638.1 linkuse as main transcript	c.277-47A>C	intron_variant			ENSP00000494412
ARID5B	ENST00000681100.1 linkuse as main transcript	c.277-47A>C	intron_variant			ENSP00000506119

Frequencies

GnomAD3 genomes

AF:

0.631

AC:

95906

AN:

151910

Hom.:

30674

Cov.:

show subpopulations

Gnomad AFR

AF:

0.720

Gnomad AMI

AF:

0.640

Gnomad AMR

AF:

0.528

Gnomad ASJ

AF:

0.599

Gnomad EAS

AF:

0.627

Gnomad SAS

AF:

0.393

Gnomad FIN

AF:

0.686

Gnomad MID

AF:

0.567

Gnomad NFE

AF:

0.613

Gnomad OTH

AF:

0.600

GnomAD3 exomes

AF:

0.578

AC:

143164

AN:

247868

Hom.:

42429

AF XY:

0.568

AC XY:

76032

AN XY:

133970

show subpopulations

Gnomad AFR exome

AF:

0.722

Gnomad AMR exome

AF:

0.495

Gnomad ASJ exome

AF:

0.579

Gnomad EAS exome

AF:

0.612

Gnomad SAS exome

AF:

0.380

Gnomad FIN exome

AF:

0.684

Gnomad NFE exome

AF:

0.609

Gnomad OTH exome

AF:

0.598

GnomAD4 exome

AF:

0.591

AC:

844202

AN:

1427604

Hom.:

252994

Cov.:

AF XY:

0.585

AC XY:

416436

AN XY:

711894

show subpopulations

Gnomad4 AFR exome

AF:

0.724

Gnomad4 AMR exome

AF:

0.494

Gnomad4 ASJ exome

AF:

0.584

Gnomad4 EAS exome

AF:

0.632

Gnomad4 SAS exome

AF:

0.381

Gnomad4 FIN exome

AF:

0.689

Gnomad4 NFE exome

AF:

0.602

Gnomad4 OTH exome

AF:

0.588

GnomAD4 genome

AF:

0.631

AC:

95997

AN:

152028

Hom.:

30714

Cov.:

AF XY:

0.628

AC XY:

46645

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.720

Gnomad4 AMR

AF:

0.528

Gnomad4 ASJ

AF:

0.599

Gnomad4 EAS

AF:

0.627

Gnomad4 SAS

AF:

0.391

Gnomad4 FIN

AF:

0.686

Gnomad4 NFE

AF:

0.612

Gnomad4 OTH

AF:

0.604

Alfa

AF:

0.604

Hom.:

59735

Bravo

AF:

0.624

Asia WGS

AF:

0.590

AC:

2052

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.18

DANN

Benign

0.50

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over