dbSNP rs733905: TRGV6:p.Ile70Val (chr7-38340845-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.56

Publications

8 publications found

Variant links:

COSMIC-nc: COSV68900407

Genes affected

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

TRGV6 links:

TRG (HGNC:12271):

TRG links:

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

TRG-AS1 links:

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new If you want to explore the variant's impact on the transcript ENST00000000000, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
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.:

show subpopulations

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.:

AF XY:

0.104

AC XY:

22296

AN XY:

214500

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1664

3329

4993

6658

8322

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

226

452

678

904

1130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.191

AC:

28882

AN:

151600

Hom.:

4256

Cov.:

AF XY:

0.183

AC XY:

13593

AN XY:

74104

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.108

AC:

7332

AN:

67936

Other (OTH)

AF:

0.184

AC:

387

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1001

2002

3003

4004

5005

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

278

556

834

1112

1390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over