15-74655977-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_025083.5(EDC3):c.576C>T(p.Phe192=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000923 in 1,613,816 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000086 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000093 ( 2 hom. )
Consequence
EDC3
NM_025083.5 synonymous
NM_025083.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.147
Genes affected
EDC3 (HGNC:26114): (enhancer of mRNA decapping 3) This gene encodes a protein that is important in mRNA degradation. The encoded protein is a component of a decapping complex that promotes efficient removal of the monomethylguanosine (m7G) cap from mRNAs, as part of the 5' to 3' mRNA decay pathway. Mutations in this gene have been identified in human patients with an autosomal recessive form of intellectual disability. [provided by RefSeq, May 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 15-74655977-G-A is Benign according to our data. Variant chr15-74655977-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2645543.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.147 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDC3 | NM_025083.5 | c.576C>T | p.Phe192= | synonymous_variant | 4/7 | ENST00000315127.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDC3 | ENST00000315127.9 | c.576C>T | p.Phe192= | synonymous_variant | 4/7 | 1 | NM_025083.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000856 AC: 13AN: 151810Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000231 AC: 58AN: 251450Hom.: 0 AF XY: 0.000294 AC XY: 40AN XY: 135894
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GnomAD4 exome AF: 0.0000930 AC: 136AN: 1461888Hom.: 2 Cov.: 32 AF XY: 0.000140 AC XY: 102AN XY: 727244
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GnomAD4 genome ? AF: 0.0000856 AC: 13AN: 151928Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74246
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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 | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | EDC3: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at