10-63191092-G-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_032776.3(JMJD1C):c.6093C>G(p.Thr2031Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T2031T) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
JMJD1C
NM_032776.3 synonymous
NM_032776.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.426
Publications
1 publications found
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]
JMJD1C Gene-Disease associations (from GenCC):
- 22q11.2 deletion syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- complex neurodevelopmental disorderInheritance: AD Classification: LIMITED Submitted by: Illumina
- neurodevelopmental disorderInheritance: AD Classification: LIMITED Submitted by: G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.031).
BP7
Synonymous conserved (PhyloP=0.426 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_032776.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| JMJD1C | NM_032776.3 | MANE Select | c.6093C>G | p.Thr2031Thr | synonymous | Exon 17 of 26 | NP_116165.1 | ||
| JMJD1C | NM_001322252.2 | c.5979C>G | p.Thr1993Thr | synonymous | Exon 16 of 25 | NP_001309181.1 | |||
| JMJD1C | NM_001282948.2 | c.5547C>G | p.Thr1849Thr | synonymous | Exon 16 of 25 | NP_001269877.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| JMJD1C | ENST00000399262.7 | TSL:5 MANE Select | c.6093C>G | p.Thr2031Thr | synonymous | Exon 17 of 26 | ENSP00000382204.2 | ||
| JMJD1C | ENST00000542921.5 | TSL:1 | c.5547C>G | p.Thr1849Thr | synonymous | Exon 16 of 25 | ENSP00000444682.1 | ||
| JMJD1C | ENST00000402544.5 | TSL:1 | n.5809C>G | non_coding_transcript_exon | Exon 13 of 22 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152134Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152134
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:
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459954Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726452 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1459954
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
726452
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33412
American (AMR)
AF:
AC:
0
AN:
44676
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26122
East Asian (EAS)
AF:
AC:
0
AN:
39686
South Asian (SAS)
AF:
AC:
0
AN:
86202
European-Finnish (FIN)
AF:
AC:
0
AN:
53418
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1110380
Other (OTH)
AF:
AC:
0
AN:
60290
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
GnomAD4 genome 0.0000131 AC: 2AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152134
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
74328
show subpopulations
African (AFR)
AF:
AC:
2
AN:
41428
American (AMR)
AF:
AC:
0
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5194
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10608
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68032
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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