10-63465485-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032776.3(JMJD1C):c.168+10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.993 in 1,592,154 control chromosomes in the GnomAD database, including 785,457 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.96 ( 70903 hom., cov: 34)
Exomes 𝑓: 1.0 ( 714554 hom. )
Consequence
JMJD1C
NM_032776.3 intron
NM_032776.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.20
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 10-63465485-A-G is Benign according to our data. Variant chr10-63465485-A-G is described in ClinVar as [Benign]. Clinvar id is 1164927.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.168+10T>C | intron_variant | ENST00000399262.7 | NP_116165.1 | |||
JMJD1C-AS1 | NR_027182.1 | n.257A>G | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.168+10T>C | intron_variant | 5 | NM_032776.3 | ENSP00000382204 | ||||
JMJD1C-AS1 | ENST00000609436.1 | n.257A>G | non_coding_transcript_exon_variant | 1/1 | ||||||
JMJD1C | ENST00000633035.1 | n.113+56253T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.963 AC: 146628AN: 152208Hom.: 70852 Cov.: 34
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GnomAD3 exomes AF: 0.990 AC: 216064AN: 218256Hom.: 107054 AF XY: 0.992 AC XY: 118918AN XY: 119894
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GnomAD4 exome AF: 0.996 AC: 1434146AN: 1439828Hom.: 714554 Cov.: 41 AF XY: 0.997 AC XY: 712348AN XY: 714838
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GnomAD4 genome AF: 0.963 AC: 146738AN: 152326Hom.: 70903 Cov.: 34 AF XY: 0.964 AC XY: 71816AN XY: 74498
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 06, 2021 | - - |
Early myoclonic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
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