NM_032199.3:c.734-9617C>T

Variant names:

• chr10-62041271-C-T
• rs7902146
• NM_032199.3:c.734-9617C>T

Variant summary

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

The NM_032199.3(ARID5B):​c.734-9617C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151,968 control chromosomes in the GnomAD database, including 35,816 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 0.68 (35816 hom., cov: 31)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 16 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.738 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.734-9617C>T		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.734-9617C>T		intron	N/A	ENSP00000279873.7	Q14865-1
	ARID5B	ENST00000681100.1		c.734-9617C>T		intron	N/A	ENSP00000506119.1	A0A7P0TAD2

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103565 AN: 151850 Hom.: 35826 Cov.: 31

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.682 AC: 103587 AN: 151968 Hom.: 35816 Cov.: 31 AF XY: 0.681 AC XY: 50620 AN XY: 74300

African (AFR) AF: 0.588 AC: 24329 AN: 41386

American (AMR) AF: 0.592 AC: 9037 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2403 AN: 3470

East Asian (EAS) AF: 0.699 AC: 3615 AN: 5168

South Asian (SAS) AF: 0.680 AC: 3277 AN: 4816

European-Finnish (FIN) AF: 0.762 AC: 8046 AN: 10560

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50515 AN: 67980

Other (OTH) AF: 0.660 AC: 1397 AN: 2116

Alfa AF: 0.715 Hom.: 141180

Bravo AF: 0.663

Asia WGS AF: 0.616 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.35
DANN	Benign	0.77
PhyloP100		-0.73
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: rs7902146; hg19: chr10-63801030;