chr10-63168150-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032776.3(JMJD1C):c.7534-16T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000742 in 1,347,386 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 (★).
Frequency
Consequence
NM_032776.3 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.7534-16T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.7534-16T>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_032776.3 | ||||
JMJD1C | ENST00000542921.5 | c.6988-16T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
JMJD1C | ENST00000402544.5 | n.7250-41T>C | intron_variant, non_coding_transcript_variant | 1 | |||||
JMJD1C | ENST00000467356.5 | n.392-16T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 7.42e-7 AC: 1AN: 1347386Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 676578
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.