rs1561966

chr11-118350759-G-Achr11-118350759-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000073.3(CD3G):c.439+76G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 1,607,790 control chromosomes in the GnomAD database, including 88,238 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.32 (8141 hom., cov: 28)
  • Exomes 𝑓: 0.32 (80097 hom.)
• Consequence: CD3G NM_000073.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD3G	NM_000073.3	c.439+76G>A		intron_variant		ENST00000532917.3
CD3G	XM_005271724.5	c.515G>A	p.Trp172Ter	stop_gained	4/4
CD3G	XM_006718941.4	c.439+76G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD3G	ENST00000532917.3	c.439+76G>A		intron_variant		1	NM_000073.3	P1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48505 AN: 151050 Hom.: 8135 Cov.: 28

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.323 AC: 470114 AN: 1456622 Hom.: 80097 Cov.: 35 AF XY: 0.329 AC XY: 238467 AN XY: 724684

Gnomad4 AFR exome AF: 0.324

Gnomad4 AMR exome AF: 0.207

Gnomad4 ASJ exome AF: 0.354

Gnomad4 EAS exome AF: 0.580

Gnomad4 SAS exome AF: 0.520

Gnomad4 FIN exome AF: 0.305

Gnomad4 NFE exome AF: 0.302

Gnomad4 OTH exome AF: 0.339

GnomAD4 genome AF: 0.321 AC: 48552 AN: 151168 Hom.: 8141 Cov.: 28 AF XY: 0.328 AC XY: 24197 AN XY: 73846

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.299

Alfa AF: 0.307 Hom.: 9847

Bravo AF: 0.313

Asia WGS AF: 0.529 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.2
Dann	Benign	0.40

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: rs1561966; hg19: chr11-118221474;