NM_032199.3:c.1102-3273G>T

Variant names:

• chr10-62066427-G-T
• rs9415636
• NM_032199.3:c.1102-3273G>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.1102-3273G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.059 in 152,212 control chromosomes in the GnomAD database, including 374 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 0.059 (374 hom., cov: 32)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.1102-3273G>T		intron_variant	Intron 7 of 9	ENST00000279873.12	NP_115575.1
ARID5B	NM_001244638.2	c.373-3273G>T		intron_variant	Intron 4 of 6		NP_001231567.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID5B	ENST00000279873.12	c.1102-3273G>T		intron_variant	Intron 7 of 9	1	NM_032199.3	ENSP00000279873.7
ARID5B	ENST00000681100.1	c.1078-3273G>T		intron_variant	Intron 7 of 9			ENSP00000506119.1
ARID5B	ENST00000309334.5	c.373-3273G>T		intron_variant	Intron 4 of 6	5		ENSP00000308862.5

Frequencies

GnomAD3 genomes AF: 0.0591 AC: 8995 AN: 152094 Hom.: 375 Cov.: 32

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0564

Gnomad ASJ AF: 0.0736

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0914

Gnomad OTH AF: 0.0855

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

GnomAD4 genome AF: 0.0590 AC: 8988 AN: 152212 Hom.: 374 Cov.: 32 AF XY: 0.0569 AC XY: 4231 AN XY: 74416

African (AFR) AF: 0.0157 AC: 654 AN: 41536

American (AMR) AF: 0.0562 AC: 859 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0736 AC: 255 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0299 AC: 144 AN: 4824

European-Finnish (FIN) AF: 0.0512 AC: 542 AN: 10596

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0914 AC: 6213 AN: 67992

Other (OTH) AF: 0.0846 AC: 179 AN: 2116

Alfa AF: 0.0731 Hom.: 427

Bravo AF: 0.0577

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.5
DANN	Benign	0.73
PhyloP100		0.075
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9415636; hg19: chr10-63826186;