rs1404794797
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_032776.3(JMJD1C):c.4763C>T(p.Ala1588Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000746 in 1,607,992 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1588D) has been classified as Uncertain significance.
Frequency
Consequence
NM_032776.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.4763C>T | p.Ala1588Val | missense_variant | 10/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.4763C>T | p.Ala1588Val | missense_variant | 10/26 | 5 | NM_032776.3 | ||
JMJD1C | ENST00000542921.5 | c.4217C>T | p.Ala1406Val | missense_variant | 9/25 | 1 | P1 | ||
JMJD1C | ENST00000402544.5 | n.4735C>T | non_coding_transcript_exon_variant | 7/22 | 1 | ||||
JMJD1C | ENST00000327520.7 | c.821C>T | p.Ala274Val | missense_variant | 1/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248170Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134714
GnomAD4 exome AF: 0.00000687 AC: 10AN: 1455848Hom.: 0 Cov.: 31 AF XY: 0.00000828 AC XY: 6AN XY: 724600
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 20, 2021 | 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with JMJD1C-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with valine at codon 1588 of the JMJD1C protein (p.Ala1588Val). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and valine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at