chr12-6975270-T-C
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_006331.8(EMG1):āc.513T>Cā(p.Cys171=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00212 in 1,613,564 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0017 ( 1 hom., cov: 33)
Exomes š: 0.0022 ( 64 hom. )
Consequence
EMG1
NM_006331.8 synonymous
NM_006331.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.851
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=-0.59).
BP6
Variant 12-6975270-T-C is Benign according to our data. Variant chr12-6975270-T-C is described in ClinVar as [Benign]. Clinvar id is 726527.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.851 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00169 (258/152372) while in subpopulation SAS AF= 0.0308 (149/4830). AF 95% confidence interval is 0.0268. There are 1 homozygotes in gnomad4. There are 159 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 64 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EMG1 | NM_006331.8 | c.513T>C | p.Cys171= | synonymous_variant | 5/6 | ENST00000599672.6 | |
EMG1 | NM_001320049.2 | c.471+122T>C | intron_variant | ||||
EMG1 | NR_135131.2 | n.524T>C | non_coding_transcript_exon_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMG1 | ENST00000599672.6 | c.513T>C | p.Cys171= | synonymous_variant | 5/6 | 1 | NM_006331.8 | P1 | |
EMG1 | ENST00000539196.2 | c.334+122T>C | intron_variant | 2 | |||||
EMG1 | ENST00000611981.1 | n.920T>C | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00170 AC: 259AN: 152254Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00494 AC: 1225AN: 247770Hom.: 25 AF XY: 0.00570 AC XY: 766AN XY: 134484
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GnomAD4 exome AF: 0.00217 AC: 3169AN: 1461192Hom.: 64 Cov.: 32 AF XY: 0.00275 AC XY: 1996AN XY: 726836
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GnomAD4 genome AF: 0.00169 AC: 258AN: 152372Hom.: 1 Cov.: 33 AF XY: 0.00213 AC XY: 159AN XY: 74520
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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
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at