rs733905

Variant names:

• chr7-38340845-T-C
• rs733905
• unassigned_transcript_1234:c.208A>G

Variant summary

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

The ENST00000000000(TRGV6):​c.208A>G​(p.Ile70Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 525,722 control chromosomes in the GnomAD database, including 7,285 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.19 (4256 hom., cov: 28)
  • Exomes 𝑓: 0.11 (3029 hom.)
• Consequence: TRGV6 ENST00000000000 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.56
• Publications: 8 publications found

Genes affected

TRGV6 (HGNC:12292): (T cell receptor gamma variable 6 (pseudogene))

TRG (HGNC:12271):

TRG-AS1 (HGNC:48974): (T cell receptor gamma locus antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417928.1. 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
	TRGV6	ENST00000417928.1	TSL:6	n.154A>G		non_coding_transcript_exon	Exon 1 of 1
	TRG-AS1	ENST00000685545.1		n.396+4019T>C		intron	N/A
	TRG-AS1	ENST00000687516.1		n.541-1411T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28855 AN: 151482 Hom.: 4250 Cov.: 28

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0777

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.107 AC: 40084 AN: 374122 Hom.: 3029 Cov.: 0 AF XY: 0.104 AC XY: 22296 AN XY: 214500

African (AFR) AF: 0.426 AC: 4470 AN: 10486

American (AMR) AF: 0.0871 AC: 3180 AN: 36496

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 1699 AN: 11930

East Asian (EAS) AF: 0.106 AC: 1456 AN: 13752

South Asian (SAS) AF: 0.0762 AC: 5154 AN: 67604

European-Finnish (FIN) AF: 0.0357 AC: 656 AN: 18382

Middle Eastern (MID) AF: 0.233 AC: 545 AN: 2344

European-Non Finnish (NFE) AF: 0.107 AC: 20909 AN: 196150

Other (OTH) AF: 0.119 AC: 2015 AN: 16978

GnomAD4 genome AF: 0.191 AC: 28882 AN: 151600 Hom.: 4256 Cov.: 28 AF XY: 0.183 AC XY: 13593 AN XY: 74104

African (AFR) AF: 0.415 AC: 17080 AN: 41120

American (AMR) AF: 0.142 AC: 2165 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 477 AN: 3464

East Asian (EAS) AF: 0.127 AC: 655 AN: 5164

South Asian (SAS) AF: 0.0777 AC: 373 AN: 4798

European-Finnish (FIN) AF: 0.0292 AC: 309 AN: 10584

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7332 AN: 67936

Other (OTH) AF: 0.184 AC: 387 AN: 2102

Alfa AF: 0.144 Hom.: 6799

Bravo AF: 0.213

Asia WGS AF: 0.117 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.048
DANN	Benign	0.30
PhyloP100		-5.6

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs733905; hg19: chr7-38380446; COSMIC: COSV68900407;