rs183013953
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_032776.3(JMJD1C):c.4567A>T(p.Ile1523Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,614,228 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. I1523I) has been classified as Likely benign.
Frequency
Consequence
NM_032776.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.4567A>T | p.Ile1523Phe | missense_variant | 10/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.4567A>T | p.Ile1523Phe | missense_variant | 10/26 | 5 | NM_032776.3 | ||
JMJD1C | ENST00000542921.5 | c.4021A>T | p.Ile1341Phe | missense_variant | 9/25 | 1 | P1 | ||
JMJD1C | ENST00000402544.5 | n.4539A>T | non_coding_transcript_exon_variant | 7/22 | 1 | ||||
JMJD1C | ENST00000327520.7 | c.625A>T | p.Ile209Phe | missense_variant | 1/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000690 AC: 105AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000164 AC: 41AN: 249428Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135322
GnomAD4 exome AF: 0.0000602 AC: 88AN: 1461874Hom.: 0 Cov.: 33 AF XY: 0.0000605 AC XY: 44AN XY: 727232
GnomAD4 genome AF: 0.000689 AC: 105AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.000604 AC XY: 45AN XY: 74508
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at