rs112116567
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_032776.3(JMJD1C):āc.2037T>Cā(p.His679=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000933 in 1,614,186 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00072 ( 0 hom., cov: 32)
Exomes š: 0.00095 ( 9 hom. )
Consequence
JMJD1C
NM_032776.3 synonymous
NM_032776.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.26
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 -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant 10-63214130-A-G is Benign according to our data. Variant chr10-63214130-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 529722.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.26 with no splicing effect.
BS2
?
High AC in GnomAd4 at 110 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.2037T>C | p.His679= | synonymous_variant | 8/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.2037T>C | p.His679= | synonymous_variant | 8/26 | 5 | NM_032776.3 | ||
JMJD1C | ENST00000542921.5 | c.1491T>C | p.His497= | synonymous_variant | 7/25 | 1 | P1 | ||
JMJD1C | ENST00000402544.5 | n.2009T>C | non_coding_transcript_exon_variant | 5/22 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000710 AC: 108AN: 152198Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000956 AC: 238AN: 249062Hom.: 3 AF XY: 0.00104 AC XY: 141AN XY: 135094
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GnomAD4 exome AF: 0.000955 AC: 1396AN: 1461870Hom.: 9 Cov.: 33 AF XY: 0.00103 AC XY: 746AN XY: 727230
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GnomAD4 genome ? AF: 0.000722 AC: 110AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000698 AC XY: 52AN XY: 74478
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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:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | JMJD1C: BS1, BS2 - |
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Computational scores
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BayesDel_noAF
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