rs200728992
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_032776.3(JMJD1C):āc.966A>Gā(p.Pro322=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000991 in 1,614,132 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 (ā ).
Frequency
Genomes: š 0.00054 ( 0 hom., cov: 32)
Exomes š: 0.000053 ( 0 hom. )
Consequence
JMJD1C
NM_032776.3 synonymous
NM_032776.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.29
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 10-63215312-T-C is Benign according to our data. Variant chr10-63215312-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 460284.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.29 with no splicing effect.
BS2
?
High AC in GnomAd4 at 82 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.966A>G | p.Pro322= | synonymous_variant | 7/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.966A>G | p.Pro322= | synonymous_variant | 7/26 | 5 | NM_032776.3 | ||
JMJD1C | ENST00000542921.5 | c.420A>G | p.Pro140= | synonymous_variant | 6/25 | 1 | P1 | ||
JMJD1C | ENST00000402544.5 | n.938A>G | non_coding_transcript_exon_variant | 4/22 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000539 AC: 82AN: 152212Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
82
AN:
152212
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000140 AC: 35AN: 249454Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135344
GnomAD3 exomes
AF:
AC:
35
AN:
249454
Hom.:
AF XY:
AC XY:
15
AN XY:
135344
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461802Hom.: 0 Cov.: 33 AF XY: 0.0000440 AC XY: 32AN XY: 727198
GnomAD4 exome
AF:
AC:
78
AN:
1461802
Hom.:
Cov.:
33
AF XY:
AC XY:
32
AN XY:
727198
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000538 AC: 82AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.000389 AC XY: 29AN XY: 74506
GnomAD4 genome
?
AF:
AC:
82
AN:
152330
Hom.:
Cov.:
32
AF XY:
AC XY:
29
AN XY:
74506
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
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 | Aug 04, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at