dbSNP rs17274: TRB:n.142407445C>T (chr7-142407445-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Consequence

TRB
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.524

Variant links:

Genes affected

TRB (HGNC:12155):

TRB links:

TRBV11-1 (HGNC:12180): (T cell receptor beta variable 11-1) Predicted to be involved in cell surface receptor signaling pathway. Predicted to be part of T cell receptor complex. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TRBV11-1 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRB		n.142407445C>T		intragenic_variant
TRBV11-1	unassigned_transcript_1344	c.-244C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRBV11-1	ENST00000390367.3 link	c.-244C>T		upstream_gene_variant		6		ENSP00000374890.3		A0A0K0K1C0

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

Alfa

AF:

0.244

Hom.:

2246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD