rs2893881

Variant names:

• chr10-61928913-G-A
• rs2893881
• NM_032199.3:c.277-11270G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-61928913-G-A
• chr10-61928913-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032199.3(ARID5B):​c.277-11270G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,100 control chromosomes in the GnomAD database, including 49,727 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 0.81 (49727 hom., cov: 31)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.602
• Publications: 14 publications found

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 Gene-Disease associations (from GenCC):

• isolated cleft palate

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.277-11270G>A		intron_variant	Intron 2 of 9	ENST00000279873.12	NP_115575.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID5B	ENST00000279873.12	c.277-11270G>A		intron_variant	Intron 2 of 9	1	NM_032199.3	ENSP00000279873.7
ARID5B	ENST00000644638.1	c.277-11270G>A		intron_variant	Intron 2 of 4			ENSP00000494412.1
ARID5B	ENST00000681100.1	c.277-11270G>A		intron_variant	Intron 2 of 9			ENSP00000506119.1

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122664 AN: 151982 Hom.: 49703 Cov.: 31

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.807 AC: 122735 AN: 152100 Hom.: 49727 Cov.: 31 AF XY: 0.804 AC XY: 59790 AN XY: 74338

African (AFR) AF: 0.758 AC: 31416 AN: 41460

American (AMR) AF: 0.732 AC: 11179 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2953 AN: 3472

East Asian (EAS) AF: 0.694 AC: 3584 AN: 5166

South Asian (SAS) AF: 0.806 AC: 3889 AN: 4824

European-Finnish (FIN) AF: 0.840 AC: 8882 AN: 10572

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58098 AN: 68012

Other (OTH) AF: 0.800 AC: 1685 AN: 2106

Alfa AF: 0.836 Hom.: 229157

Bravo AF: 0.796

Asia WGS AF: 0.786 AC: 2733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		0.60
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2893881; hg19: chr10-63688672;