chr6-15307653-C-T

Position:

• chr6-15307653-C-T

Variant summary

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

The ENST00000341776.7(JARID2):​c.45+61069C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,180 control chromosomes in the GnomAD database, including 1,637 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 0.12 (1637 hom., cov: 32)
• Consequence: JARID2 ENST00000341776.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JARID2	NM_004973.4	c.45+61069C>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.45+61069C>T		intron_variant		1	NM_004973.4	ENSP00000341280	P2
JARID2	ENST00000397311.4	c.-472+58689C>T		intron_variant		2		ENSP00000380478	A2

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18860 AN: 152062 Hom.: 1627 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0701

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0720

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.124 AC: 18907 AN: 152180 Hom.: 1637 Cov.: 32 AF XY: 0.126 AC XY: 9343 AN XY: 74398

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.0699

Gnomad4 ASJ AF: 0.0600

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.0758

Gnomad4 NFE AF: 0.0720

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0895 Hom.: 443

Bravo AF: 0.126

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.54

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: rs16876210; hg19: chr6-15307884;