rs778255192
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032776.3(JMJD1C):c.4358C>T(p.Thr1453Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000479 in 1,461,296 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T1453T) has been classified as Benign.
Frequency
Consequence
NM_032776.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.4358C>T | p.Thr1453Ile | missense_variant | 10/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.4358C>T | p.Thr1453Ile | missense_variant | 10/26 | 5 | NM_032776.3 | ||
JMJD1C | ENST00000542921.5 | c.3812C>T | p.Thr1271Ile | missense_variant | 9/25 | 1 | P1 | ||
JMJD1C | ENST00000402544.5 | n.4330C>T | non_coding_transcript_exon_variant | 7/22 | 1 | ||||
JMJD1C | ENST00000327520.7 | c.416C>T | p.Thr139Ile | missense_variant | 1/12 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248656Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134966
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461296Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727000
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 23, 2021 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 460246). This variant has not been reported in the literature in individuals affected with JMJD1C-related conditions. This variant is present in population databases (rs778255192, gnomAD 0.01%). This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 1453 of the JMJD1C protein (p.Thr1453Ile). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at