11-118344360-AGGCT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000073.3(CD3G):c.-46_-43del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,387,408 control chromosomes in the GnomAD database, including 72,888 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.32 (8033 hom., cov: 0)
  • Exomes 𝑓: 0.31 (64855 hom.)
• Consequence: CD3G NM_000073.3 5_prime_UTR
• Clinical Significance: Benign/Likely benign criteria provided, single submitter B:2
• Conservation: PhyloP100: 0.00

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-118344360-AGGCT-A is Benign according to our data. Variant chr11-118344360-AGGCT-A is described in ClinVar as [Likely_benign]. Clinvar id is 302678.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD3G	NM_000073.3	c.-46_-43del		5_prime_UTR_variant	1/7	ENST00000532917.3
CD3G	XM_005271724.5	c.-46_-43del		5_prime_UTR_variant	1/4
CD3G	XM_006718941.4	c.-46_-43del		5_prime_UTR_variant	1/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD3G	ENST00000532917.3	c.-46_-43del		5_prime_UTR_variant	1/7	1	NM_000073.3	P1

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48484 AN: 151670 Hom.: 8026 Cov.: 0

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.311 AC: 384148 AN: 1235620 Hom.: 64855 AF XY: 0.318 AC XY: 196522 AN XY: 617050

Gnomad4 AFR exome AF: 0.322

Gnomad4 AMR exome AF: 0.208

Gnomad4 ASJ exome AF: 0.352

Gnomad4 EAS exome AF: 0.556

Gnomad4 SAS exome AF: 0.513

Gnomad4 FIN exome AF: 0.305

Gnomad4 NFE exome AF: 0.287

Gnomad4 OTH exome AF: 0.325

GnomAD4 genome AF: 0.320 AC: 48534 AN: 151788 Hom.: 8033 Cov.: 0 AF XY: 0.326 AC XY: 24172 AN XY: 74172

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.292

Alfa AF: 0.176 Hom.: 333

Bravo AF: 0.311

Asia WGS AF: 0.518 AC: 1801 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

Submissions by phenotype

Immunodeficiency due to defect in CD3-gamma Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Severe combined immunodeficiency disease Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs60810919; hg19: chr11-118215075;