rs3778651

Positions:

• chr6-15518301-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004973.4(JARID2):​c.3558+1033C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,182 control chromosomes in the GnomAD database, including 1,143 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 0.11 (1143 hom., cov: 33)
• Consequence: JARID2 NM_004973.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

Genes affected

JARID2 (HGNC:6196): (jumonji and AT-rich interaction domain containing 2) This gene encodes a Jumonji- and AT-rich interaction domain (ARID)-domain-containing protein. The encoded protein is a DNA-binding protein that functions as a transcriptional repressor. This protein interacts with the Polycomb repressive complex 2 (PRC2) which plays an essential role in regulating gene expression during embryonic development. This protein facilitates the recruitment of the PRC2 complex to target genes. Alternate splicing results in multiple transcript variants. Mutations in this gene are associated with chronic myeloid malignancies. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JARID2	NM_004973.4	c.3558+1033C>T		intron_variant		ENST00000341776.7	NP_004964.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JARID2	ENST00000341776.7	c.3558+1033C>T		intron_variant		1	NM_004973.4	ENSP00000341280	P2
JARID2	ENST00000397311.4	c.3042+1033C>T		intron_variant		2		ENSP00000380478	A2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16822 AN: 152064 Hom.: 1146 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0698

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.111 AC: 16836 AN: 152182 Hom.: 1143 Cov.: 33 AF XY: 0.111 AC XY: 8237 AN XY: 74404

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0663

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0586

Gnomad4 NFE AF: 0.0698

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0811 Hom.: 294

Bravo AF: 0.120

Asia WGS AF: 0.170 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3778651; hg19: chr6-15518532;