rs528244230
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_032776.3(JMJD1C):āc.1112A>Gā(p.Asn371Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000803 in 1,607,060 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_032776.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.1112A>G | p.Asn371Ser | missense_variant | 8/26 | ENST00000399262.7 | NP_116165.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.1112A>G | p.Asn371Ser | missense_variant | 8/26 | 5 | NM_032776.3 | ENSP00000382204 | ||
JMJD1C | ENST00000542921.5 | c.566A>G | p.Asn189Ser | missense_variant | 7/25 | 1 | ENSP00000444682 | P1 | ||
JMJD1C | ENST00000402544.5 | n.1084A>G | non_coding_transcript_exon_variant | 5/22 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 39AN: 243570Hom.: 0 AF XY: 0.000182 AC XY: 24AN XY: 132102
GnomAD4 exome AF: 0.0000845 AC: 123AN: 1454770Hom.: 1 Cov.: 32 AF XY: 0.0000857 AC XY: 62AN XY: 723320
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74486
ClinVar
Submissions by phenotype
Early myoclonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at