rs7923074

Variant names:

• chr10-61963681-A-C
• rs7923074
• NM_032199.3:c.502+23273A>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.502+23273A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,500 control chromosomes in the GnomAD database, including 23,567 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 0.56 (23567 hom., cov: 30)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032199.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID5B	NM_032199.3	MANE Select	c.502+23273A>C		intron	N/A	NP_115575.1	Q14865-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID5B	ENST00000279873.12	TSL:1 MANE Select	c.502+23273A>C		intron	N/A	ENSP00000279873.7	Q14865-1
	ARID5B	ENST00000644638.1		c.502+23273A>C		intron	N/A	ENSP00000494412.1	A0A2R8Y5F2
	ARID5B	ENST00000681100.1		c.502+23273A>C		intron	N/A	ENSP00000506119.1	A0A7P0TAD2

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84224 AN: 151382 Hom.: 23565 Cov.: 30

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.556 AC: 84257 AN: 151500 Hom.: 23567 Cov.: 30 AF XY: 0.554 AC XY: 41015 AN XY: 74018

African (AFR) AF: 0.525 AC: 21654 AN: 41248

American (AMR) AF: 0.485 AC: 7347 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1976 AN: 3466

East Asian (EAS) AF: 0.503 AC: 2583 AN: 5140

South Asian (SAS) AF: 0.444 AC: 2129 AN: 4796

European-Finnish (FIN) AF: 0.617 AC: 6471 AN: 10486

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40185 AN: 67896

Other (OTH) AF: 0.557 AC: 1174 AN: 2106

Alfa AF: 0.571 Hom.: 3937

Bravo AF: 0.544

Asia WGS AF: 0.530 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		0.13
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: rs7923074; hg19: chr10-63723440;