11-118344489-ACTAGGGGTCTGG-GGCTATCATTCTTCTTCAAGGTAAGGGCCTTC

Position:

• chr11-118344489-ACTAGGGGTCTGG-GGCTATCATTCTTCTTCAAGGTAAGGGCCTTC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000073.3(CD3G):​c.55+11_55+23delinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CD3G NM_000073.3 intron
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.92

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD3G	NM_000073.3	c.55+11_55+23delinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC		intron_variant		ENST00000532917.3
CD3G	XM_005271724.5	c.55+11_55+23delinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC		intron_variant
CD3G	XM_006718941.4	c.55+11_55+23delinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD3G	ENST00000532917.3	c.55+11_55+23delinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC		intron_variant		1	NM_000073.3	P1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Combined immunodeficiency due to CD3gamma deficiency Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 26, 2022

This sequence change falls in intron 1 of the CD3G gene. It does not directly change the encoded amino acid sequence of the CD3G protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CD3G-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the effect of this variant on mRNA splicing is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-118215204;