rs7765425

Positions:

• chr6-15327842-G-A
• chr6-15327842-G-T

Variant summary

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

The NM_004973.4(JARID2):​c.46-46275G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0846 in 152,156 control chromosomes in the GnomAD database, including 749 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 0.085 (749 hom., cov: 32)
• Consequence: JARID2 NM_004973.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JARID2	NM_004973.4	c.46-46275G>A		intron_variant		ENST00000341776.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JARID2	ENST00000341776.7	c.46-46275G>A		intron_variant		1	NM_004973.4	P2
JARID2	ENST00000397311.4	c.-471-46275G>A		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.0844 AC: 12836 AN: 152038 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.0534

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0422

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0546

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0846 AC: 12875 AN: 152156 Hom.: 749 Cov.: 32 AF XY: 0.0851 AC XY: 6334 AN XY: 74400

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0528

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.0535

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0422

Gnomad4 NFE AF: 0.0547

Gnomad4 OTH AF: 0.0856

Alfa AF: 0.0565 Hom.: 390

Bravo AF: 0.0866

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs7765425; hg19: chr6-15328073;