chr10-61935289-C-G

Variant names:

• chr10-61935289-C-G
• rs6479779
• NM_032199.3:c.277-4894C>G

Variant summary

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

The NM_032199.3(ARID5B):​c.277-4894C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,832 control chromosomes in the GnomAD database, including 29,788 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 0.62 (29788 hom., cov: 30)
• Consequence: ARID5B NM_032199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 5 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=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID5B	NM_032199.3	c.277-4894C>G		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.277-4894C>G		intron_variant	Intron 2 of 9	1	NM_032199.3	ENSP00000279873.7
ARID5B	ENST00000644638.1	c.277-4894C>G		intron_variant	Intron 2 of 4			ENSP00000494412.1
ARID5B	ENST00000681100.1	c.277-4894C>G		intron_variant	Intron 2 of 9			ENSP00000506119.1

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94823 AN: 151716 Hom.: 29774 Cov.: 30

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.625 AC: 94874 AN: 151832 Hom.: 29788 Cov.: 30 AF XY: 0.625 AC XY: 46374 AN XY: 74176

African (AFR) AF: 0.614 AC: 25419 AN: 41370

American (AMR) AF: 0.575 AC: 8783 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2035 AN: 3470

East Asian (EAS) AF: 0.622 AC: 3208 AN: 5154

South Asian (SAS) AF: 0.489 AC: 2350 AN: 4808

European-Finnish (FIN) AF: 0.720 AC: 7564 AN: 10506

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.641 AC: 43562 AN: 67946

Other (OTH) AF: 0.604 AC: 1272 AN: 2106

Alfa AF: 0.567 Hom.: 1782

Bravo AF: 0.614

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		0.17
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: rs6479779; hg19: chr10-63695048;