15-74632618-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_025083.5(EDC3):c.1521T>C(p.Ser507=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,613,482 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 0.00010 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000048 ( 2 hom. )
Consequence
EDC3
NM_025083.5 synonymous
NM_025083.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.40
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]
CLK3 (HGNC:2071): (CDC like kinase 3) This gene encodes a protein belonging to the serine/threonine type protein kinase family. This protein is a nuclear dual-specificity kinase that regulates the intranuclear distribution of the serine/arginine-rich (SR) family of splicing factors. Two transcript variants encoding different isoforms have been found for this gene. Related pseudogenes are located on chromosomes 1 and 9. [provided by RefSeq, Jul 2008]
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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=-0.75).
BP6
?
Variant 15-74632618-A-G is Benign according to our data. Variant chr15-74632618-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 756592.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.4 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDC3 | NM_025083.5 | c.1521T>C | p.Ser507= | synonymous_variant | 7/7 | ENST00000315127.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDC3 | ENST00000315127.9 | c.1521T>C | p.Ser507= | synonymous_variant | 7/7 | 1 | NM_025083.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152272Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000207 AC: 52AN: 251146Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135802
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GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461092Hom.: 2 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 726826
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GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152390Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74530
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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 | Invitae | Jul 10, 2018 | - - |
Computational scores
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Benign
Cadd
Benign
Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at