chr6-15468645-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_004973.4(JARID2):c.597C>T(p.Thr199Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00691 in 1,613,882 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0054 ( 4 hom., cov: 30)
Exomes 𝑓: 0.0071 ( 59 hom. )
Consequence
JARID2
NM_004973.4 synonymous
NM_004973.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.90
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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 6-15468645-C-T is Benign according to our data. Variant chr6-15468645-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 788355.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.9 with no splicing effect.
BS2
High AC in GnomAd4 at 816 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JARID2 | ENST00000341776.7 | c.597C>T | p.Thr199Thr | synonymous_variant | Exon 5 of 18 | 1 | NM_004973.4 | ENSP00000341280.2 | ||
JARID2 | ENST00000397311.4 | c.81C>T | p.Thr27Thr | synonymous_variant | Exon 5 of 18 | 2 | ENSP00000380478.3 |
Frequencies
GnomAD3 genomes AF: 0.00537 AC: 816AN: 152034Hom.: 4 Cov.: 30
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GnomAD3 exomes AF: 0.00613 AC: 1541AN: 251236Hom.: 14 AF XY: 0.00629 AC XY: 854AN XY: 135784
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GnomAD4 exome AF: 0.00707 AC: 10335AN: 1461730Hom.: 59 Cov.: 32 AF XY: 0.00699 AC XY: 5081AN XY: 727154
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GnomAD4 genome AF: 0.00536 AC: 816AN: 152152Hom.: 4 Cov.: 30 AF XY: 0.00573 AC XY: 426AN XY: 74382
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2025 | JARID2: BP4, BP7, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
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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