NM_000073.3:c.55+11_55+23delACTAGGGGTCTGGinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC

Variant names:

• chr11-118344489-ACTAGGGGTCTGG-GGCTATCATTCTTCTTCAAGGTAAGGGCCTTC
• NM_000073.3:c.55+11_55+23delACTAGGGGTCTGGinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000073.3(CD3G):​c.55+11_55+23delACTAGGGGTCTGGinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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
• 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 deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000073.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD3G	NM_000073.3	MANE Select	c.55+11_55+23delACTAGGGGTCTGGinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC		intron	N/A	NP_000064.1	P09693
	CD3G	NM_001440319.1		c.55+11_55+23delACTAGGGGTCTGGinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC		intron	N/A	NP_001427248.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD3G	ENST00000532917.3	TSL:1 MANE Select	c.55+11_55+23delACTAGGGGTCTGGinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC		intron	N/A	ENSP00000431445.2	P09693
	CD3G	ENST00000528540.5	TSL:1	c.-109+11_-109+23delACTAGGGGTCTGGinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC		intron	N/A	ENSP00000498162.1	A0A3B3IUD8
	CD3G	ENST00000292144.8	TSL:1	n.55+11_55+23delACTAGGGGTCTGGinsGGCTATCATTCTTCTTCAAGGTAAGGGCCTTC		intron	N/A	ENSP00000292144.4	J3KNA5

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

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	Combined immunodeficiency due to CD3gamma deficiency (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.9

Splicing

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

Other links and lift over

hg19: chr11-118215204;