rs201464655
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_032776.3(JMJD1C):c.1703A>T(p.Asp568Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00153 in 1,614,010 control chromosomes in the GnomAD database, including 3 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D568G) has been classified as Uncertain significance.
Frequency
Consequence
NM_032776.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.1703A>T | p.Asp568Val | missense_variant | 8/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.1703A>T | p.Asp568Val | missense_variant | 8/26 | 5 | NM_032776.3 | ||
JMJD1C | ENST00000542921.5 | c.1157A>T | p.Asp386Val | missense_variant | 7/25 | 1 | P1 | ||
JMJD1C | ENST00000402544.5 | n.1675A>T | non_coding_transcript_exon_variant | 5/22 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000874 AC: 133AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000944 AC: 235AN: 248850Hom.: 0 AF XY: 0.000933 AC XY: 126AN XY: 134988
GnomAD4 exome AF: 0.00159 AC: 2330AN: 1461658Hom.: 3 Cov.: 33 AF XY: 0.00152 AC XY: 1103AN XY: 727136
GnomAD4 genome ? AF: 0.000873 AC: 133AN: 152352Hom.: 0 Cov.: 32 AF XY: 0.000631 AC XY: 47AN XY: 74512
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at