10-61911100-C-G

Variant names:

• chr10-61911100-C-G
• rs2393782
• NM_032199.3:c.276+8687C>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.276+8687C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,238 control chromosomes in the GnomAD database, including 58,917 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 0.88 (58917 hom., cov: 33)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66
• Publications: 3 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)

ENSG00000307546 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 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.276+8687C>G		intron	N/A	NP_115575.1	Q14865-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID5B	ENST00000279873.12	TSL:1 MANE Select	c.276+8687C>G		intron	N/A	ENSP00000279873.7	Q14865-1
	ARID5B	ENST00000644638.1		c.276+8687C>G		intron	N/A	ENSP00000494412.1	A0A2R8Y5F2
	ARID5B	ENST00000681100.1		c.276+8687C>G		intron	N/A	ENSP00000506119.1	A0A7P0TAD2

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133374 AN: 152120 Hom.: 58875 Cov.: 33

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.838

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.877 AC: 133474 AN: 152238 Hom.: 58917 Cov.: 33 AF XY: 0.869 AC XY: 64691 AN XY: 74410

African (AFR) AF: 0.962 AC: 39968 AN: 41568

American (AMR) AF: 0.758 AC: 11593 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2948 AN: 3472

East Asian (EAS) AF: 0.697 AC: 3605 AN: 5170

South Asian (SAS) AF: 0.843 AC: 4069 AN: 4828

European-Finnish (FIN) AF: 0.800 AC: 8458 AN: 10574

Middle Eastern (MID) AF: 0.836 AC: 244 AN: 292

European-Non Finnish (NFE) AF: 0.882 AC: 60028 AN: 68022

Other (OTH) AF: 0.858 AC: 1811 AN: 2110

Alfa AF: 0.883 Hom.: 6948

Bravo AF: 0.875

Asia WGS AF: 0.806 AC: 2801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	14
DANN	Benign	0.74
PhyloP100		1.7
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: rs2393782; hg19: chr10-63670859;