chr10-61937857-C-G

Variant names:

• chr10-61937857-C-G
• rs2893880
• NM_032199.3:c.277-2326C>G

Variant summary

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

The NM_032199.3(ARID5B):​c.277-2326C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,000 control chromosomes in the GnomAD database, including 36,250 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 0.69 (36250 hom., cov: 31)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032199.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID5B	NM_032199.3	MANE Select	c.277-2326C>G		intron	N/A	NP_115575.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID5B	ENST00000279873.12	TSL:1 MANE Select	c.277-2326C>G		intron	N/A	ENSP00000279873.7
	ARID5B	ENST00000644638.1		c.277-2326C>G		intron	N/A	ENSP00000494412.1
	ARID5B	ENST00000681100.1		c.277-2326C>G		intron	N/A	ENSP00000506119.1

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104678 AN: 151882 Hom.: 36229 Cov.: 31

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.689 AC: 104744 AN: 152000 Hom.: 36250 Cov.: 31 AF XY: 0.689 AC XY: 51174 AN XY: 74300

African (AFR) AF: 0.692 AC: 28669 AN: 41452

American (AMR) AF: 0.581 AC: 8869 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2375 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3366 AN: 5146

South Asian (SAS) AF: 0.578 AC: 2788 AN: 4820

European-Finnish (FIN) AF: 0.794 AC: 8390 AN: 10570

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48018 AN: 67962

Other (OTH) AF: 0.674 AC: 1424 AN: 2112

Alfa AF: 0.652 Hom.: 2027

Bravo AF: 0.670

Asia WGS AF: 0.682 AC: 2374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.60
PhyloP100		-1.2
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: rs2893880; hg19: chr10-63697616;