rs771233853
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_032776.3(JMJD1C):c.6522G>A(p.Lys2174=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000757 in 1,612,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000079 ( 0 hom. )
Consequence
JMJD1C
NM_032776.3 synonymous
NM_032776.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.15
Genes affected
JMJD1C (HGNC:12313): (jumonji domain containing 1C) The protein encoded by this gene interacts with thyroid hormone receptors and contains a jumonji domain. It is a candidate histone demethylase and is thought to be a coactivator for key transcription factors. It plays a role in the DNA-damage response pathway by demethylating the mediator of DNA damage checkpoint 1 (MDC1) protein, and is required for the survival of acute myeloid leukemia. Mutations in this gene are associated with Rett syndrome and intellectual disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 10-63189216-C-T is Benign according to our data. Variant chr10-63189216-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 460267.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.15 with no splicing effect.
BS2
High AC in GnomAd4 at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.6522G>A | p.Lys2174= | synonymous_variant | 18/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.6522G>A | p.Lys2174= | synonymous_variant | 18/26 | 5 | NM_032776.3 | ||
JMJD1C | ENST00000542921.5 | c.5976G>A | p.Lys1992= | synonymous_variant | 17/25 | 1 | P1 | ||
JMJD1C | ENST00000402544.5 | n.6238G>A | non_coding_transcript_exon_variant | 14/22 | 1 | ||||
JMJD1C | ENST00000327520.7 | c.2163G>A | p.Lys721= | synonymous_variant | 7/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152148Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248510Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134904
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GnomAD4 exome AF: 0.0000787 AC: 115AN: 1460432Hom.: 0 Cov.: 30 AF XY: 0.0000798 AC XY: 58AN XY: 726628
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74326
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 11, 2023 | - - |
Computational scores
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Name
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Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at