rs754194693
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032776.3(JMJD1C):c.5400G>T(p.Glu1800Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000275 in 1,452,106 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.5400G>T | p.Glu1800Asp | missense_variant | 12/26 | ENST00000399262.7 | NP_116165.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.5400G>T | p.Glu1800Asp | missense_variant | 12/26 | 5 | NM_032776.3 | ENSP00000382204 | ||
JMJD1C | ENST00000542921.5 | c.4854G>T | p.Glu1618Asp | missense_variant | 11/25 | 1 | ENSP00000444682 | P1 | ||
JMJD1C | ENST00000402544.5 | n.5170G>T | non_coding_transcript_exon_variant | 8/22 | 1 | |||||
JMJD1C | ENST00000327520.7 | c.1132-1041G>T | intron_variant | 2 | ENSP00000335929 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248536Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134858
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1452106Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1AN XY: 723108
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 31, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at