rs733905

Positions:

• chr7-38340845-T-C

Variant summary

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

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. 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 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.56

Genes affected

TRGV6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRGV6	unassigned_transcript_1234	c.208A>G	p.Ile70Val	missense_variant	2/2
TRG		n.38340845T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRGV6	ENST00000417928.1	n.154A>G		non_coding_transcript_exon_variant	1/1	6
TRG-AS1	ENST00000685545.1	n.396+4019T>C		intron_variant
TRG-AS1	ENST00000687516.1	n.541-1411T>C		intron_variant

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

Gnomad4 AFR exome AF: 0.426

Gnomad4 AMR exome AF: 0.0871

Gnomad4 ASJ exome AF: 0.142

Gnomad4 EAS exome AF: 0.106

Gnomad4 SAS exome AF: 0.0762

Gnomad4 FIN exome AF: 0.0357

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 0.119

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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0777

Gnomad4 FIN AF: 0.0292

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.184

Alfa AF: 0.124 Hom.: 2862

Bravo AF: 0.213

Asia WGS AF: 0.117 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

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