rs9654600

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004973.4(JARID2):​c.3450+460T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,316 control chromosomes in the GnomAD database, including 1,234 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 ( 1234 hom., cov: 34)

Consequence

JARID2
NM_004973.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.39
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
JARID2NM_004973.4 linkuse as main transcriptc.3450+460T>A intron_variant ENST00000341776.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
JARID2ENST00000341776.7 linkuse as main transcriptc.3450+460T>A intron_variant 1 NM_004973.4 P2Q92833-1
JARID2ENST00000397311.4 linkuse as main transcriptc.2934+460T>A intron_variant 2 A2Q92833-3

Frequencies

GnomAD3 genomes
AF:
0.115
AC:
17539
AN:
152198
Hom.:
1237
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.181
Gnomad AMI
AF:
0.0592
Gnomad AMR
AF:
0.128
Gnomad ASJ
AF:
0.0688
Gnomad EAS
AF:
0.235
Gnomad SAS
AF:
0.118
Gnomad FIN
AF:
0.0589
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.0748
Gnomad OTH
AF:
0.113
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.115
AC:
17556
AN:
152316
Hom.:
1234
Cov.:
34
AF XY:
0.115
AC XY:
8561
AN XY:
74478
show subpopulations
Gnomad4 AFR
AF:
0.181
Gnomad4 AMR
AF:
0.128
Gnomad4 ASJ
AF:
0.0688
Gnomad4 EAS
AF:
0.235
Gnomad4 SAS
AF:
0.119
Gnomad4 FIN
AF:
0.0589
Gnomad4 NFE
AF:
0.0748
Gnomad4 OTH
AF:
0.115
Alfa
AF:
0.0157
Hom.:
5
Bravo
AF:
0.125
Asia WGS
AF:
0.172
AC:
598
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
6.1
DANN
Benign
0.44

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9654600; hg19: chr6-15514113; API