rs200368807
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_032776.3(JMJD1C):āc.6427A>Gā(p.Ile2143Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000459 in 1,613,926 control chromosomes in the GnomAD database, including 1 homozygotes. 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.6427A>G | p.Ile2143Val | missense_variant | 18/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.6427A>G | p.Ile2143Val | missense_variant | 18/26 | 5 | NM_032776.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000486 AC: 74AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000642 AC: 160AN: 249396Hom.: 0 AF XY: 0.000621 AC XY: 84AN XY: 135314
GnomAD4 exome AF: 0.000456 AC: 666AN: 1461552Hom.: 1 Cov.: 31 AF XY: 0.000459 AC XY: 334AN XY: 727100
GnomAD4 genome ? AF: 0.000486 AC: 74AN: 152374Hom.: 0 Cov.: 32 AF XY: 0.000577 AC XY: 43AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.6427A>G (p.I2143V) alteration is located in exon 18 (coding exon 18) of the JMJD1C gene. This alteration results from a A to G substitution at nucleotide position 6427, causing the isoleucine (I) at amino acid position 2143 to be replaced by a valine (V). 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 | Oct 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at