chr10-61910106-C-A

Variant names:

• chr10-61910106-C-A
• rs4948487
• NM_032199.3:c.276+7693C>A

Variant summary

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

The NM_032199.3(ARID5B):​c.276+7693C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,022 control chromosomes in the GnomAD database, including 19,127 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 0.50 (19127 hom., cov: 32)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.276+7693C>A		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.276+7693C>A		intron_variant	Intron 2 of 9	1	NM_032199.3	ENSP00000279873.7
ARID5B	ENST00000644638.1	c.276+7693C>A		intron_variant	Intron 2 of 4			ENSP00000494412.1
ARID5B	ENST00000681100.1	c.276+7693C>A		intron_variant	Intron 2 of 9			ENSP00000506119.1

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75476 AN: 151904 Hom.: 19092 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.497 AC: 75566 AN: 152022 Hom.: 19127 Cov.: 32 AF XY: 0.493 AC XY: 36611 AN XY: 74278

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.489

Alfa AF: 0.467 Hom.: 15709

Bravo AF: 0.493

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.4
DANN	Benign	0.51

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: rs4948487; hg19: chr10-63669865;