rs17231

Positions:

• chr7-142415520-C-A

Variant summary

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

The ENST00000479785.1(TRBV12-1):​n.198C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 214,286 control chromosomes in the GnomAD database, including 15,045 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 0.34 (10157 hom., cov: 31)
  • Exomes 𝑓: 0.38 (4888 hom.)
• Consequence: TRBV12-1 ENST00000479785.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

Genes affected

TRBV12-1 (HGNC:12183): (T cell receptor beta variable 12-1 (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.462 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
TRBV12-1	ENST00000479785.1	n.198C>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51116 AN: 151844 Hom.: 10155 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.315

GnomAD4 exome AF: 0.378 AC: 23536 AN: 62324 Hom.: 4888 Cov.: 0 AF XY: 0.378 AC XY: 13970 AN XY: 36932

Gnomad4 AFR exome AF: 0.122

Gnomad4 AMR exome AF: 0.327

Gnomad4 ASJ exome AF: 0.399

Gnomad4 EAS exome AF: 0.162

Gnomad4 SAS exome AF: 0.183

Gnomad4 FIN exome AF: 0.444

Gnomad4 NFE exome AF: 0.461

Gnomad4 OTH exome AF: 0.431

GnomAD4 genome AF: 0.336 AC: 51127 AN: 151962 Hom.: 10157 Cov.: 31 AF XY: 0.331 AC XY: 24568 AN XY: 74268

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.312

Alfa AF: 0.402 Hom.: 6734

Bravo AF: 0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17231; hg19: chr7-142216436;