11-118344360-AGGCTGGCT-A
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_000073.3(CD3G):c.-50_-43delGCTGGCTG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000323 in 1,237,622 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000032 ( 0 hom. )
Consequence
CD3G
NM_000073.3 5_prime_UTR
NM_000073.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.137
Publications
0 publications found
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]
CD3G Gene-Disease associations (from GenCC):
- combined immunodeficiency due to CD3gamma deficiencyInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CD3G | NM_000073.3 | c.-50_-43delGCTGGCTG | 5_prime_UTR_variant | Exon 1 of 7 | ENST00000532917.3 | NP_000064.1 | ||
| CD3G | NM_001440319.1 | c.-50_-43delGCTGGCTG | 5_prime_UTR_variant | Exon 1 of 7 | NP_001427248.1 | |||
| CD3G | XM_005271724.5 | c.-50_-43delGCTGGCTG | 5_prime_UTR_variant | Exon 1 of 4 | XP_005271781.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
0
GnomAD4 exome AF: 0.00000323 AC: 4AN: 1237622Hom.: 0 AF XY: 0.00000485 AC XY: 3AN XY: 617986 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
4
AN:
1237622
Hom.:
AF XY:
AC XY:
3
AN XY:
617986
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
28490
American (AMR)
AF:
AC:
0
AN:
35502
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24098
East Asian (EAS)
AF:
AC:
0
AN:
34828
South Asian (SAS)
AF:
AC:
0
AN:
75530
European-Finnish (FIN)
AF:
AC:
0
AN:
48882
Middle Eastern (MID)
AF:
AC:
0
AN:
5174
European-Non Finnish (NFE)
AF:
AC:
4
AN:
932624
Other (OTH)
AF:
AC:
0
AN:
52494
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
0
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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