rs201371848
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_032776.3(JMJD1C):āc.1166T>Cā(p.Ile389Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000456 in 1,601,206 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032776.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.1166T>C | p.Ile389Thr | missense_variant | 8/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.1166T>C | p.Ile389Thr | missense_variant | 8/26 | 5 | NM_032776.3 | ||
JMJD1C | ENST00000542921.5 | c.620T>C | p.Ile207Thr | missense_variant | 7/25 | 1 | P1 | ||
JMJD1C | ENST00000402544.5 | n.1138T>C | non_coding_transcript_exon_variant | 5/22 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000316 AC: 48AN: 151882Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000656 AC: 16AN: 243790Hom.: 0 AF XY: 0.0000530 AC XY: 7AN XY: 132166
GnomAD4 exome AF: 0.0000172 AC: 25AN: 1449324Hom.: 0 Cov.: 32 AF XY: 0.0000139 AC XY: 10AN XY: 720994
GnomAD4 genome ? AF: 0.000316 AC: 48AN: 151882Hom.: 0 Cov.: 32 AF XY: 0.000324 AC XY: 24AN XY: 74180
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2022 | The c.1166T>C (p.I389T) alteration is located in exon 8 (coding exon 8) of the JMJD1C gene. This alteration results from a T to C substitution at nucleotide position 1166, causing the isoleucine (I) at amino acid position 389 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at