chr10-63168063-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_032776.3(JMJD1C):c.7605G>C(p.Glu2535Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 1,584,334 control chromosomes in the GnomAD database, including 173,701 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
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.7605G>C | p.Glu2535Asp | missense_variant | 26/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.7605G>C | p.Glu2535Asp | missense_variant | 26/26 | 5 | NM_032776.3 | ||
JMJD1C | ENST00000542921.5 | c.7059G>C | p.Glu2353Asp | missense_variant | 25/25 | 1 | P1 | ||
JMJD1C | ENST00000402544.5 | n.7296G>C | non_coding_transcript_exon_variant | 22/22 | 1 | ||||
JMJD1C | ENST00000467356.5 | n.463G>C | non_coding_transcript_exon_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.428 AC: 64991AN: 151814Hom.: 14546 Cov.: 32
GnomAD3 exomes AF: 0.438 AC: 108928AN: 248440Hom.: 25300 AF XY: 0.452 AC XY: 61012AN XY: 134850
GnomAD4 exome AF: 0.467 AC: 668979AN: 1432402Hom.: 159169 Cov.: 27 AF XY: 0.472 AC XY: 337084AN XY: 714480
GnomAD4 genome ? AF: 0.428 AC: 64963AN: 151932Hom.: 14532 Cov.: 32 AF XY: 0.428 AC XY: 31758AN XY: 74254
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