rs17231

Variant names:

• chr7-142415520-C-A
• rs17231
• unassigned_transcript_1345:c.198C>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000000000(TRBV12-1):​c.198C>A​(p.Tyr66*) variant causes a stop gained 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 ENST00000000000 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 6 publications found

Genes affected

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

TRB (HGNC:12155):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• 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 rank	MANE	Protein	UniProt
TRBV12-1	unassigned_transcript_1345	c.198C>A	p.Tyr66*	stop_gained	Exon 2 of 2
TRB		n.142415520C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRBV12-1	ENST00000479785.1	n.198C>A		non_coding_transcript_exon_variant	Exon 2 of 2	6

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

African (AFR) AF: 0.122 AC: 230 AN: 1882

American (AMR) AF: 0.327 AC: 2915 AN: 8928

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 379 AN: 950

East Asian (EAS) AF: 0.162 AC: 642 AN: 3956

South Asian (SAS) AF: 0.183 AC: 1277 AN: 6986

European-Finnish (FIN) AF: 0.444 AC: 2003 AN: 4516

Middle Eastern (MID) AF: 0.258 AC: 17 AN: 66

European-Non Finnish (NFE) AF: 0.461 AC: 15054 AN: 32678

Other (OTH) AF: 0.431 AC: 1019 AN: 2362

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

African (AFR) AF: 0.132 AC: 5463 AN: 41484

American (AMR) AF: 0.351 AC: 5351 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1344 AN: 3468

East Asian (EAS) AF: 0.181 AC: 933 AN: 5162

South Asian (SAS) AF: 0.182 AC: 875 AN: 4818

European-Finnish (FIN) AF: 0.420 AC: 4422 AN: 10540

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31645 AN: 67922

Other (OTH) AF: 0.312 AC: 657 AN: 2106

Alfa AF: 0.406 Hom.: 7501

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs17231; hg19: chr7-142216436;