rs41274072
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_032776.3(JMJD1C):c.1771A>G(p.Met591Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0326 in 1,613,846 control chromosomes in the GnomAD database, including 1,181 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.1771A>G | p.Met591Val | missense_variant | 8/26 | ENST00000399262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.1771A>G | p.Met591Val | missense_variant | 8/26 | 5 | NM_032776.3 | ||
JMJD1C | ENST00000542921.5 | c.1225A>G | p.Met409Val | missense_variant | 7/25 | 1 | P1 | ||
JMJD1C | ENST00000402544.5 | n.1743A>G | non_coding_transcript_exon_variant | 5/22 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0510 AC: 7769AN: 152220Hom.: 293 Cov.: 32
GnomAD3 exomes AF: 0.0289 AC: 7204AN: 248896Hom.: 223 AF XY: 0.0267 AC XY: 3601AN XY: 135032
GnomAD4 exome AF: 0.0306 AC: 44768AN: 1461508Hom.: 883 Cov.: 33 AF XY: 0.0295 AC XY: 21441AN XY: 727070
GnomAD4 genome ? AF: 0.0512 AC: 7796AN: 152338Hom.: 298 Cov.: 32 AF XY: 0.0498 AC XY: 3711AN XY: 74504
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at