rs71508903

Variant names:

• chr10-62020112-C-T
• rs71508903
• NM_032199.3:c.733+19791C>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.733+19791C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,110 control chromosomes in the GnomAD database, including 2,125 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 0.15 (2125 hom., cov: 31)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• Publications: 41 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 (EAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.733+19791C>T		intron_variant	Intron 4 of 9	ENST00000279873.12	NP_115575.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID5B	ENST00000279873.12	c.733+19791C>T		intron_variant	Intron 4 of 9	1	NM_032199.3	ENSP00000279873.7
ARID5B	ENST00000644638.1	c.734-4561C>T		intron_variant	Intron 4 of 4			ENSP00000494412.1
ARID5B	ENST00000681100.1	c.733+19791C>T		intron_variant	Intron 4 of 9			ENSP00000506119.1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23123 AN: 151992 Hom.: 2120 Cov.: 31

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.152 AC: 23136 AN: 152110 Hom.: 2125 Cov.: 31 AF XY: 0.153 AC XY: 11375 AN XY: 74358

African (AFR) AF: 0.0405 AC: 1682 AN: 41510

American (AMR) AF: 0.196 AC: 3000 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3472

East Asian (EAS) AF: 0.213 AC: 1106 AN: 5186

South Asian (SAS) AF: 0.185 AC: 890 AN: 4808

European-Finnish (FIN) AF: 0.183 AC: 1935 AN: 10582

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13130 AN: 67972

Other (OTH) AF: 0.185 AC: 391 AN: 2110

Alfa AF: 0.178 Hom.: 5526

Bravo AF: 0.148

Asia WGS AF: 0.243 AC: 843 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	14
DANN	Benign	0.74
PhyloP100		0.44
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: rs71508903; hg19: chr10-63779871;