rs718880

chr7-38322398-G-A

Variant summary

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

The 7-38322398-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,020 control chromosomes in the GnomAD database, including 1,499 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 0.12 (1498 hom., cov: 29)
  • Exomes 𝑓: 0.073 (1 hom.)
• Consequence: TRGVA ENST00000413819.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

Genes affected

TRGVA (HGNC:12296): (T cell receptor gamma variable A (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRGVA	ENST00000413819.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18329 AN: 151806 Hom.: 1496 Cov.: 29

Gnomad AFR AF: 0.0582

Gnomad AMI AF: 0.0808

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.132

GnomAD4 exome AF: 0.0729 AC: 7 AN: 96 Hom.: 1 Cov.: 0 AF XY: 0.0750 AC XY: 6 AN XY: 80

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0694

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.121 AC: 18346 AN: 151924 Hom.: 1498 Cov.: 29 AF XY: 0.126 AC XY: 9357 AN XY: 74266

Gnomad4 AFR AF: 0.0584

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.0957

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.131

Alfa AF: 0.118 Hom.: 2337

Bravo AF: 0.121

Asia WGS AF: 0.263 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.7
Dann	Benign	0.55

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: rs718880; hg19: chr7-38361999;