rs706

Positions:

• chr7-142802078-A-G

Variant summary

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

The ENST00000466254.1(TRBC2):​c.406-27A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 766,058 control chromosomes in the GnomAD database, including 52,829 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 0.36 (10525 hom., cov: 31)
  • Exomes 𝑓: 0.36 (42304 hom.)
• Consequence: TRBC2 ENST00000466254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942

Genes affected

TRBC2 (HGNC:12157): (T cell receptor beta constant 2) Predicted to enable antigen binding activity and immunoglobulin receptor binding activity. Predicted to be involved in several processes, including activation of immune response; defense response to other organism; and phagocytosis. Predicted to be integral component of membrane. Predicted to be part of immunoglobulin complex, circulating. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRBC2	ENST00000466254.1	c.406-27A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55335 AN: 151824 Hom.: 10507 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.363

GnomAD3 exomes AF: 0.342 AC: 80160 AN: 234590 Hom.: 14846 AF XY: 0.340 AC XY: 43603 AN XY: 128216

Gnomad AFR exome AF: 0.315

Gnomad AMR exome AF: 0.306

Gnomad ASJ exome AF: 0.323

Gnomad EAS exome AF: 0.167

Gnomad SAS exome AF: 0.206

Gnomad FIN exome AF: 0.418

Gnomad NFE exome AF: 0.415

Gnomad OTH exome AF: 0.365

GnomAD4 exome AF: 0.359 AC: 220597 AN: 614116 Hom.: 42304 Cov.: 0 AF XY: 0.352 AC XY: 118157 AN XY: 335598

Gnomad4 AFR exome AF: 0.320

Gnomad4 AMR exome AF: 0.309

Gnomad4 ASJ exome AF: 0.325

Gnomad4 EAS exome AF: 0.156

Gnomad4 SAS exome AF: 0.211

Gnomad4 FIN exome AF: 0.421

Gnomad4 NFE exome AF: 0.413

Gnomad4 OTH exome AF: 0.364

GnomAD4 genome AF: 0.365 AC: 55389 AN: 151942 Hom.: 10525 Cov.: 31 AF XY: 0.359 AC XY: 26661 AN XY: 74270

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.360

Alfa AF: 0.378 Hom.: 1114

Bravo AF: 0.362

Asia WGS AF: 0.190 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.34
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs706; hg19: chr7-142499762; COSMIC: COSV66585745;