10-63465607-A-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_032776.3(JMJD1C):c.56T>A(p.Val19Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000436 in 1,609,330 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. V19V) has been classified as Likely benign.
Frequency
Consequence
NM_032776.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.56T>A | p.Val19Asp | missense_variant | 1/26 | ENST00000399262.7 | |
JMJD1C-AS1 | NR_027182.1 | n.379A>T | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.56T>A | p.Val19Asp | missense_variant | 1/26 | 5 | NM_032776.3 | ||
JMJD1C-AS1 | ENST00000609436.1 | n.379A>T | non_coding_transcript_exon_variant | 1/1 | |||||
JMJD1C | ENST00000633035.1 | n.113+56131T>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00232 AC: 352AN: 151890Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000580 AC: 139AN: 239512Hom.: 0 AF XY: 0.000442 AC XY: 58AN XY: 131194
GnomAD4 exome AF: 0.000242 AC: 352AN: 1457322Hom.: 2 Cov.: 36 AF XY: 0.000186 AC XY: 135AN XY: 725270
GnomAD4 genome AF: 0.00230 AC: 349AN: 152008Hom.: 2 Cov.: 33 AF XY: 0.00206 AC XY: 153AN XY: 74304
ClinVar
Submissions by phenotype
JMJD1C-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at