chr12-6975333-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_006331.8(EMG1):c.576C>T(p.Ser192=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00405 in 1,607,664 control chromosomes in the GnomAD database, including 207 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.020 ( 107 hom., cov: 33)
Exomes 𝑓: 0.0024 ( 100 hom. )
Consequence
EMG1
NM_006331.8 synonymous
NM_006331.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0930
Genes affected
EMG1 (HGNC:16912): (EMG1 N1-specific pseudouridine methyltransferase) This gene encodes an essential, conserved eukaryotic protein that methylates pseudouridine in 18S rRNA. The related protein in yeast is a component of the small subunit processome and is essential for biogenesis of the ribosomal 40S subunit. A mutation in this gene has been associated with Bowen-Conradi syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 12-6975333-C-T is Benign according to our data. Variant chr12-6975333-C-T is described in ClinVar as [Benign]. Clinvar id is 781063.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.093 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0663 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EMG1 | NM_006331.8 | c.576C>T | p.Ser192= | synonymous_variant | 5/6 | ENST00000599672.6 | |
EMG1 | NM_001320049.2 | c.471+185C>T | intron_variant | ||||
EMG1 | NR_135131.2 | n.587C>T | non_coding_transcript_exon_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMG1 | ENST00000599672.6 | c.576C>T | p.Ser192= | synonymous_variant | 5/6 | 1 | NM_006331.8 | P1 | |
EMG1 | ENST00000539196.2 | c.334+185C>T | intron_variant | 2 | |||||
EMG1 | ENST00000611981.1 | n.983C>T | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0197 AC: 3004AN: 152248Hom.: 106 Cov.: 33
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GnomAD3 exomes AF: 0.00531 AC: 1258AN: 236766Hom.: 32 AF XY: 0.00420 AC XY: 539AN XY: 128248
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GnomAD4 exome AF: 0.00241 AC: 3504AN: 1455298Hom.: 100 Cov.: 32 AF XY: 0.00210 AC XY: 1517AN XY: 723282
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GnomAD4 genome AF: 0.0198 AC: 3014AN: 152366Hom.: 107 Cov.: 33 AF XY: 0.0196 AC XY: 1461AN XY: 74512
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at