rs706

Variant names:

• chr7-142802078-A-G
• rs706
• ENST00000466254.1:c.404-27A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000466254.1(TRBC2):​c.404-27A>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
• Publications: 11 publications found

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]

TRB (HGNC:12155):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000466254.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRBC2	ENST00000466254.1	TSL:6	c.404-27A>G		intron	N/A	ENSP00000417300.1	A0A5H1ZRR3

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

GnomAD2 exomes AF: 0.342 AC: 80160 AN: 234590 AF XY: 0.340

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 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

African (AFR) AF: 0.320 AC: 5653 AN: 17690

American (AMR) AF: 0.309 AC: 13498 AN: 43734

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 6820 AN: 20984

East Asian (EAS) AF: 0.156 AC: 5621 AN: 36066

South Asian (SAS) AF: 0.211 AC: 14746 AN: 69798

European-Finnish (FIN) AF: 0.421 AC: 16359 AN: 38848

Middle Eastern (MID) AF: 0.342 AC: 1416 AN: 4142

European-Non Finnish (NFE) AF: 0.413 AC: 144488 AN: 349868

Other (OTH) AF: 0.364 AC: 11996 AN: 32986

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

African (AFR) AF: 0.324 AC: 13417 AN: 41424

American (AMR) AF: 0.361 AC: 5511 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1166 AN: 3464

East Asian (EAS) AF: 0.163 AC: 843 AN: 5158

South Asian (SAS) AF: 0.189 AC: 909 AN: 4816

European-Finnish (FIN) AF: 0.401 AC: 4237 AN: 10554

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.413 AC: 28069 AN: 67932

Other (OTH) AF: 0.360 AC: 758 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.34
DANN	Benign	0.37
PhyloP100		-0.94
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs706;

hg19: chr7-142499762;

COSMIC: COSV66585745;