rs2235258
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004973.4(JARID2):c.3279G>A(p.Leu1093=) variant causes a synonymous change. The variant allele was found at a frequency of 0.739 in 1,568,922 control chromosomes in the GnomAD database, including 434,832 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 0.65 ( 34247 hom., cov: 34)
Exomes 𝑓: 0.75 ( 400585 hom. )
Consequence
JARID2
NM_004973.4 synonymous
NM_004973.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.52
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=-0.53).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JARID2 | NM_004973.4 | c.3279G>A | p.Leu1093= | synonymous_variant | 16/18 | ENST00000341776.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JARID2 | ENST00000341776.7 | c.3279G>A | p.Leu1093= | synonymous_variant | 16/18 | 1 | NM_004973.4 | P2 | |
JARID2 | ENST00000397311.4 | c.2763G>A | p.Leu921= | synonymous_variant | 16/18 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.647 AC: 98424AN: 152040Hom.: 34238 Cov.: 34
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GnomAD3 exomes AF: 0.722 AC: 139195AN: 192860Hom.: 51386 AF XY: 0.728 AC XY: 75385AN XY: 103506
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GnomAD4 exome AF: 0.749 AC: 1060613AN: 1416764Hom.: 400585 Cov.: 54 AF XY: 0.749 AC XY: 523986AN XY: 699684
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GnomAD4 genome ? AF: 0.647 AC: 98457AN: 152158Hom.: 34247 Cov.: 34 AF XY: 0.652 AC XY: 48489AN XY: 74402
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at