rs4245597

Variant names:

• chr10-61966183-G-A
• rs4245597
• NM_032199.3:c.502+25775G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-61966183-G-A
• chr10-61966183-G-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+25775G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,068 control chromosomes in the GnomAD database, including 37,705 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 0.70 (37705 hom., cov: 33)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.502+25775G>A		intron_variant	Intron 3 of 9	ENST00000279873.12	NP_115575.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID5B	ENST00000279873.12	c.502+25775G>A		intron_variant	Intron 3 of 9	1	NM_032199.3	ENSP00000279873.7
ARID5B	ENST00000644638.1	c.502+25775G>A		intron_variant	Intron 3 of 4			ENSP00000494412.1
ARID5B	ENST00000681100.1	c.502+25775G>A		intron_variant	Intron 3 of 9			ENSP00000506119.1

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106165 AN: 151948 Hom.: 37658 Cov.: 33

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.699 AC: 106269 AN: 152068 Hom.: 37705 Cov.: 33 AF XY: 0.696 AC XY: 51692 AN XY: 74308

African (AFR) AF: 0.814 AC: 33813 AN: 41516

American (AMR) AF: 0.563 AC: 8593 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2373 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3299 AN: 5154

South Asian (SAS) AF: 0.508 AC: 2443 AN: 4806

European-Finnish (FIN) AF: 0.739 AC: 7806 AN: 10568

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45690 AN: 67982

Other (OTH) AF: 0.673 AC: 1421 AN: 2112

Alfa AF: 0.697 Hom.: 7767

Bravo AF: 0.690

Asia WGS AF: 0.649 AC: 2259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.46
PhyloP100		0.26
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: rs4245597; hg19: chr10-63725942;