18-51176819-T-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_016626.5(MEX3C):āc.1512A>Gā(p.Thr504Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 32)
Exomes š: 0.0000096 ( 0 hom. )
Consequence
MEX3C
NM_016626.5 synonymous
NM_016626.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.925
Genes affected
MEX3C (HGNC:28040): (mex-3 RNA binding family member C) This gene encodes a member of a family of proteins with two K homology (KH) RNA-binding domains and a C-terminal RING-finger domain. The protein interacts with mRNA via the KH domains, and the protein shuttles between the nucleus and cytoplasm. Polymorphisms in this gene may contribute to hypertension. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 18-51176819-T-C is Benign according to our data. Variant chr18-51176819-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 736133.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.925 with no splicing effect.
BS2
High AC in GnomAdExome4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MEX3C | NM_016626.5 | c.1512A>G | p.Thr504Thr | synonymous_variant | 2/2 | ENST00000406189.4 | NP_057710.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MEX3C | ENST00000406189.4 | c.1512A>G | p.Thr504Thr | synonymous_variant | 2/2 | 1 | NM_016626.5 | ENSP00000385610.3 | ||
MEX3C | ENST00000591040.2 | c.*2A>G | downstream_gene_variant | 2 | ENSP00000502049.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152094Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251122Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135720
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GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461708Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727138
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74298
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 02, 2018 | - - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at