rs7922394

Variant names:

• chr10-61906932-T-C
• rs7922394
• NM_032199.3:c.276+4519T>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.276+4519T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,080 control chromosomes in the GnomAD database, including 13,310 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 0.41 (13310 hom., cov: 33)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.752
• Publications: 2 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)

ENSG00000307546 (HGNC:):

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 = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.276+4519T>C		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+4519T>C		intron_variant	Intron 2 of 9	1	NM_032199.3	ENSP00000279873.7
ARID5B	ENST00000644638.1	c.276+4519T>C		intron_variant	Intron 2 of 4			ENSP00000494412.1
ARID5B	ENST00000681100.1	c.276+4519T>C		intron_variant	Intron 2 of 9			ENSP00000506119.1
ENSG00000307546	ENST00000826996.1	n.264-873A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62970 AN: 151962 Hom.: 13309 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.414 AC: 62995 AN: 152080 Hom.: 13310 Cov.: 33 AF XY: 0.414 AC XY: 30745 AN XY: 74350

African (AFR) AF: 0.348 AC: 14436 AN: 41474

American (AMR) AF: 0.401 AC: 6130 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1547 AN: 5180

South Asian (SAS) AF: 0.356 AC: 1719 AN: 4826

European-Finnish (FIN) AF: 0.486 AC: 5121 AN: 10544

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.463 AC: 31476 AN: 67990

Other (OTH) AF: 0.421 AC: 887 AN: 2108

Alfa AF: 0.439 Hom.: 2339

Bravo AF: 0.401

Asia WGS AF: 0.340 AC: 1182 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	6.2
DANN	Benign	0.72
PhyloP100		0.75
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: rs7922394; hg19: chr10-63666691;