rs1397945403
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_032776.3(JMJD1C):āc.3093T>Gā(p.Asp1031Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,960 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032776.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.3093T>G | p.Asp1031Glu | missense_variant | 10/26 | ENST00000399262.7 | NP_116165.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.3093T>G | p.Asp1031Glu | missense_variant | 10/26 | 5 | NM_032776.3 | ENSP00000382204 | ||
JMJD1C | ENST00000542921.5 | c.2547T>G | p.Asp849Glu | missense_variant | 9/25 | 1 | ENSP00000444682 | P1 | ||
JMJD1C | ENST00000402544.5 | n.3065T>G | non_coding_transcript_exon_variant | 7/22 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248964Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135040
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461740Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727162
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 10, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt JMJD1C protein function. ClinVar contains an entry for this variant (Variation ID: 529702). This variant has not been reported in the literature in individuals affected with JMJD1C-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 1031 of the JMJD1C protein (p.Asp1031Glu). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at