chr11-110159488-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_033390.2(ZC3H12C):c.1146C>G(p.Asp382Glu) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000751 in 1,598,394 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033390.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC3H12C | NM_033390.2 | c.1146C>G | p.Asp382Glu | missense_variant, splice_region_variant | 4/6 | ENST00000278590.8 | |
ZC3H12C | NM_001411037.1 | c.1149C>G | p.Asp383Glu | missense_variant, splice_region_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H12C | ENST00000278590.8 | c.1146C>G | p.Asp382Glu | missense_variant, splice_region_variant | 4/6 | 2 | NM_033390.2 | ||
ZC3H12C | ENST00000528673.5 | c.1149C>G | p.Asp383Glu | missense_variant, splice_region_variant | 4/6 | 2 | |||
ZC3H12C | ENST00000453089.2 | c.1053C>G | p.Asp351Glu | missense_variant, splice_region_variant | 3/5 | 2 | P1 | ||
RDX | ENST00000645527.1 | c.*250+15479G>C | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000885 AC: 2AN: 226080Hom.: 0 AF XY: 0.00000821 AC XY: 1AN XY: 121790
GnomAD4 exome AF: 0.00000691 AC: 10AN: 1446200Hom.: 0 Cov.: 30 AF XY: 0.00000418 AC XY: 3AN XY: 717532
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.1146C>G (p.D382E) alteration is located in exon 4 (coding exon 4) of the ZC3H12C gene. This alteration results from a C to G substitution at nucleotide position 1146, causing the aspartic acid (D) at amino acid position 382 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at