11-118307208-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000733.4(CD3E):c.50-80C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00327 in 1,102,140 control chromosomes in the GnomAD database, including 93 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.013 ( 47 hom., cov: 31)
Exomes 𝑓: 0.0016 ( 46 hom. )
Consequence
CD3E
NM_000733.4 intron
NM_000733.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.147
Genes affected
CD3E (HGNC:1674): (CD3 epsilon subunit of T-cell receptor complex) The protein encoded by this gene is the CD3-epsilon polypeptide, which together with CD3-gamma, -delta and -zeta, and the T-cell receptor alpha/beta and gamma/delta heterodimers, forms the T-cell receptor-CD3 complex. This complex plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. The genes encoding the epsilon, gamma and delta polypeptides are located in the same cluster on chromosome 11. The epsilon polypeptide plays an essential role in T-cell development. Defects in this gene cause immunodeficiency. This gene has also been linked to a susceptibility to type I diabetes in women. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 11-118307208-C-A is Benign according to our data. Variant chr11-118307208-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1321578.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0135 (2051/152244) while in subpopulation AFR AF= 0.0476 (1975/41522). AF 95% confidence interval is 0.0458. There are 47 homozygotes in gnomad4. There are 963 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 47 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD3E | NM_000733.4 | c.50-80C>A | intron_variant | ENST00000361763.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD3E | ENST00000361763.9 | c.50-80C>A | intron_variant | 1 | NM_000733.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0134 AC: 2039AN: 152126Hom.: 47 Cov.: 31
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GnomAD4 exome AF: 0.00163 AC: 1548AN: 949896Hom.: 46 AF XY: 0.00133 AC XY: 656AN XY: 493104
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GnomAD4 genome ? AF: 0.0135 AC: 2051AN: 152244Hom.: 47 Cov.: 31 AF XY: 0.0129 AC XY: 963AN XY: 74440
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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 | GeneDx | May 11, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at