10-61928969-C-T

Variant names:

• chr10-61928969-C-T
• rs17215180
• NM_032199.3:c.277-11214C>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.277-11214C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,884 control chromosomes in the GnomAD database, including 13,860 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 0.42 (13860 hom., cov: 30)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.277-11214C>T		intron_variant	Intron 2 of 9	ENST00000279873.12	NP_115575.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID5B	ENST00000279873.12	c.277-11214C>T		intron_variant	Intron 2 of 9	1	NM_032199.3	ENSP00000279873.7
ARID5B	ENST00000644638.1	c.277-11214C>T		intron_variant	Intron 2 of 4			ENSP00000494412.1
ARID5B	ENST00000681100.1	c.277-11214C>T		intron_variant	Intron 2 of 9			ENSP00000506119.1

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63410 AN: 151766 Hom.: 13856 Cov.: 30

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.418 AC: 63420 AN: 151884 Hom.: 13860 Cov.: 30 AF XY: 0.416 AC XY: 30852 AN XY: 74236

African (AFR) AF: 0.349 AC: 14456 AN: 41398

American (AMR) AF: 0.373 AC: 5698 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3470

East Asian (EAS) AF: 0.127 AC: 654 AN: 5164

South Asian (SAS) AF: 0.288 AC: 1388 AN: 4818

European-Finnish (FIN) AF: 0.500 AC: 5255 AN: 10512

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33088 AN: 67944

Other (OTH) AF: 0.416 AC: 877 AN: 2110

Alfa AF: 0.445 Hom.: 22437

Bravo AF: 0.399

Asia WGS AF: 0.250 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.49
PhyloP100		-0.054
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: rs17215180; hg19: chr10-63688728;