10-63465618-C-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_032776.3(JMJD1C):āc.45G>Cā(p.Leu15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,610,144 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. L15L) has been classified as Likely benign.
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.45G>C | p.Leu15= | synonymous_variant | 1/26 | ENST00000399262.7 | |
JMJD1C-AS1 | NR_027182.1 | n.390C>G | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.45G>C | p.Leu15= | synonymous_variant | 1/26 | 5 | NM_032776.3 | ||
JMJD1C-AS1 | ENST00000609436.1 | n.390C>G | non_coding_transcript_exon_variant | 1/1 | |||||
JMJD1C | ENST00000633035.1 | n.113+56120G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000994 AC: 24AN: 241356Hom.: 0 AF XY: 0.0000986 AC XY: 13AN XY: 131898
GnomAD4 exome AF: 0.000157 AC: 229AN: 1457958Hom.: 1 Cov.: 36 AF XY: 0.000136 AC XY: 99AN XY: 725568
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74346
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at