chr10-63168077-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_032776.3(JMJD1C):c.7591G>A(p.Glu2531Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00696 in 1,603,916 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. E2531E) has been classified as Benign.
Frequency
Consequence
NM_032776.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.7591G>A | p.Glu2531Lys | missense_variant | 26/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.7591G>A | p.Glu2531Lys | missense_variant | 26/26 | 5 | NM_032776.3 | ||
JMJD1C | ENST00000542921.5 | c.7045G>A | p.Glu2349Lys | missense_variant | 25/25 | 1 | P1 | ||
JMJD1C | ENST00000402544.5 | n.7282G>A | non_coding_transcript_exon_variant | 22/22 | 1 | ||||
JMJD1C | ENST00000467356.5 | n.449G>A | non_coding_transcript_exon_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00470 AC: 715AN: 152116Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00421 AC: 1047AN: 248660Hom.: 7 AF XY: 0.00435 AC XY: 587AN XY: 134970
GnomAD4 exome AF: 0.00720 AC: 10445AN: 1451682Hom.: 55 Cov.: 28 AF XY: 0.00699 AC XY: 5055AN XY: 722820
GnomAD4 genome AF: 0.00469 AC: 714AN: 152234Hom.: 6 Cov.: 32 AF XY: 0.00417 AC XY: 310AN XY: 74428
ClinVar
Submissions by phenotype
JMJD1C-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 21, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | JMJD1C: BS2 - |
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at