rs144745368
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_032776.3(JMJD1C):c.663C>T(p.Ile221=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,609,436 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. I221I) has been classified as Uncertain significance.
Frequency
Consequence
NM_032776.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.663C>T | p.Ile221= | synonymous_variant | 5/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.663C>T | p.Ile221= | synonymous_variant | 5/26 | 5 | NM_032776.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151974Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000244 AC: 6AN: 246000Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133468
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1457344Hom.: 0 Cov.: 29 AF XY: 0.0000124 AC XY: 9AN XY: 724840
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74354
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at