chr10-61997361-A-T

Variant names:

• chr10-61997361-A-T
• rs10761600
• NM_032199.3:c.503-2730A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032199.3(ARID5B):​c.503-2730A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,590 control chromosomes in the GnomAD database, including 9,335 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 0.34 (9335 hom., cov: 29)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID5B	NM_032199.3	MANE Select	c.503-2730A>T		intron	N/A	NP_115575.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID5B	ENST00000279873.12	TSL:1 MANE Select	c.503-2730A>T		intron	N/A	ENSP00000279873.7
	ARID5B	ENST00000644638.1		c.503-2730A>T		intron	N/A	ENSP00000494412.1
	ARID5B	ENST00000681100.1		c.503-2730A>T		intron	N/A	ENSP00000506119.1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 51976 AN: 151474 Hom.: 9335 Cov.: 29

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.343 AC: 51977 AN: 151590 Hom.: 9335 Cov.: 29 AF XY: 0.341 AC XY: 25227 AN XY: 74022

African (AFR) AF: 0.233 AC: 9635 AN: 41318

American (AMR) AF: 0.288 AC: 4388 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1487 AN: 3462

East Asian (EAS) AF: 0.374 AC: 1931 AN: 5160

South Asian (SAS) AF: 0.255 AC: 1224 AN: 4796

European-Finnish (FIN) AF: 0.448 AC: 4685 AN: 10468

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27336 AN: 67844

Other (OTH) AF: 0.356 AC: 751 AN: 2108

Alfa AF: 0.257 Hom.: 696

Bravo AF: 0.325

Asia WGS AF: 0.312 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.80
PhyloP100		0.55
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: rs10761600; hg19: chr10-63757120;