rs200093444
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000073.3(CD3G):c.439+12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000208 in 1,613,490 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00022 ( 1 hom. )
Consequence
CD3G
NM_000073.3 intron
NM_000073.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.300
Genes affected
CD3G (HGNC:1675): (CD3 gamma subunit of T-cell receptor complex) The protein encoded by this gene is the CD3-gamma polypeptide, which together with CD3-epsilon, -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. Defects in this gene are associated with T cell immunodeficiency. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 11-118350695-C-T is Benign according to our data. Variant chr11-118350695-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 445361.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD3G | NM_000073.3 | c.439+12C>T | intron_variant | ENST00000532917.3 | |||
CD3G | XM_005271724.5 | c.451C>T | p.Leu151Phe | missense_variant | 4/4 | ||
CD3G | XM_006718941.4 | c.439+12C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD3G | ENST00000532917.3 | c.439+12C>T | intron_variant | 1 | NM_000073.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000659 AC: 10AN: 151772Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000596 AC: 15AN: 251472Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135910
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GnomAD4 exome AF: 0.000222 AC: 325AN: 1461718Hom.: 1 Cov.: 34 AF XY: 0.000205 AC XY: 149AN XY: 727158
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GnomAD4 genome ? AF: 0.0000659 AC: 10AN: 151772Hom.: 0 Cov.: 30 AF XY: 0.0000540 AC XY: 4AN XY: 74076
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 15, 2017 | - - |
Combined immunodeficiency due to CD3gamma deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 03, 2023 | - - |
Computational scores
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Name
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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