7-142415520-C-A

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000479785.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRBV12-1	ENST00000479785.1	TSL:6	n.198C>A		non_coding_transcript_exon	Exon 2 of 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

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 v4.9

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;