chr10-62065404-T-C

Variant names:

• chr10-62065404-T-C
• rs7915732
• NM_032199.3:c.1102-4296T>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.1102-4296T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.908 in 152,210 control chromosomes in the GnomAD database, including 63,637 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 0.91 (63637 hom., cov: 32)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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.1102-4296T>C		intron	N/A	NP_115575.1	Q14865-1
	ARID5B	NM_001244638.2		c.373-4296T>C		intron	N/A	NP_001231567.1	Q14865-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID5B	ENST00000279873.12	TSL:1 MANE Select	c.1102-4296T>C		intron	N/A	ENSP00000279873.7	Q14865-1
	ARID5B	ENST00000681100.1		c.1078-4296T>C		intron	N/A	ENSP00000506119.1	A0A7P0TAD2
	ARID5B	ENST00000309334.5	TSL:5	c.373-4296T>C		intron	N/A	ENSP00000308862.5	Q14865-2

Frequencies

GnomAD3 genomes AF: 0.908 AC: 138169 AN: 152092 Hom.: 63616 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.908 AC: 138243 AN: 152210 Hom.: 63637 Cov.: 32 AF XY: 0.911 AC XY: 67816 AN XY: 74422

African (AFR) AF: 0.740 AC: 30697 AN: 41476

American (AMR) AF: 0.958 AC: 14649 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3335 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5164 AN: 5166

South Asian (SAS) AF: 0.989 AC: 4776 AN: 4828

European-Finnish (FIN) AF: 0.971 AC: 10304 AN: 10616

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66168 AN: 68034

Other (OTH) AF: 0.927 AC: 1962 AN: 2116

Alfa AF: 0.875 Hom.: 22531

Bravo AF: 0.900

Asia WGS AF: 0.975 AC: 3392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.25
PhyloP100		0.056
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: rs7915732; hg19: chr10-63825163;