rs10740055

Positions:

• chr10-61958720-C-A
• chr10-61958720-C-G
• chr10-61958720-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032199.3(ARID5B):​c.502+18312C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,954 control chromosomes in the GnomAD database, including 18,242 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 0.49 (18242 hom., cov: 32)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.502+18312C>A		intron_variant		ENST00000279873.12	NP_115575.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARID5B	ENST00000279873.12	c.502+18312C>A		intron_variant		1	NM_032199.3	ENSP00000279873	P3
ARID5B	ENST00000644638.1	c.502+18312C>A		intron_variant				ENSP00000494412
ARID5B	ENST00000681100.1	c.502+18312C>A		intron_variant				ENSP00000506119

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74203 AN: 151836 Hom.: 18239 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.489 AC: 74235 AN: 151954 Hom.: 18242 Cov.: 32 AF XY: 0.487 AC XY: 36167 AN XY: 74276

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.485

Alfa AF: 0.492 Hom.: 21982

Bravo AF: 0.480

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs10740055; hg19: chr10-63718479;