chr11-118339245-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000732.6(CD3D):c.451-18T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 1,608,916 control chromosomes in the GnomAD database, including 391,699 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.62 ( 30864 hom., cov: 30)
Exomes 𝑓: 0.70 ( 360835 hom. )
Consequence
CD3D
NM_000732.6 intron
NM_000732.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.42
Genes affected
CD3D (HGNC:1673): (CD3 delta subunit of T-cell receptor complex) The protein encoded by this gene is part of the T-cell receptor/CD3 complex (TCR/CD3 complex) and is involved in T-cell development and signal transduction. The encoded membrane protein represents the delta subunit of the CD3 complex, and along with four other CD3 subunits, binds either TCR alpha/beta or TCR gamma/delta to form the TCR/CD3 complex on the surface of T-cells. Defects in this gene are a cause of severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-positive/NK-cell-positive (SCIDBNK). Two transcript variants encoding different isoforms have been found for this gene. Other variants may also exist, but the full-length natures of their transcripts has yet to be defined. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 11-118339245-A-C is Benign according to our data. Variant chr11-118339245-A-C is described in ClinVar as [Benign]. Clinvar id is 518236.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-118339245-A-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD3D | NM_000732.6 | c.451-18T>G | intron_variant | ENST00000300692.9 | |||
CD3D | NM_001040651.2 | c.319-18T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD3D | ENST00000300692.9 | c.451-18T>G | intron_variant | 1 | NM_000732.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.622 AC: 94379AN: 151724Hom.: 30874 Cov.: 30
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GnomAD3 exomes AF: 0.671 AC: 168575AN: 251394Hom.: 58124 AF XY: 0.684 AC XY: 92894AN XY: 135874
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GnomAD4 exome AF: 0.701 AC: 1020738AN: 1457074Hom.: 360835 Cov.: 33 AF XY: 0.703 AC XY: 509625AN XY: 725184
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GnomAD4 genome ? AF: 0.622 AC: 94393AN: 151842Hom.: 30864 Cov.: 30 AF XY: 0.625 AC XY: 46390AN XY: 74208
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 78% of patients studied by a panel of primary immunodeficiencies. Number of patients: 75. Only high quality variants are reported. - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Immunodeficiency 19 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Immunodeficiency 104 Benign:1
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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