rs34798625
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032776.3(JMJD1C):c.814G>A(p.Ala272Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00633 in 1,608,906 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_032776.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.814G>A | p.Ala272Thr | missense_variant | 6/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.814G>A | p.Ala272Thr | missense_variant | 6/26 | 5 | NM_032776.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0133 AC: 2027AN: 152120Hom.: 29 Cov.: 32
GnomAD3 exomes AF: 0.00678 AC: 1684AN: 248450Hom.: 17 AF XY: 0.00653 AC XY: 880AN XY: 134822
GnomAD4 exome AF: 0.00560 AC: 8161AN: 1456668Hom.: 68 Cov.: 33 AF XY: 0.00557 AC XY: 4032AN XY: 723588
GnomAD4 genome ? AF: 0.0133 AC: 2031AN: 152238Hom.: 29 Cov.: 32 AF XY: 0.0132 AC XY: 984AN XY: 74442
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at