rs718880

Variant names:

• chr7-38322398-G-A
• rs718880

Variant summary

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

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: TRG intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 6 publications found

Genes affected

TRG (HGNC:12271):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRG		n.38322398G>A		intragenic_variant
TRGVA	unassigned_transcript_1231	c.*48C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRGVA	ENST00000413819.1	n.*48C>T		downstream_gene_variant		6

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0694 AC: 5 AN: 72

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.0584 AC: 2420 AN: 41436

American (AMR) AF: 0.227 AC: 3463 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1554 AN: 5166

South Asian (SAS) AF: 0.192 AC: 925 AN: 4818

European-Finnish (FIN) AF: 0.135 AC: 1428 AN: 10548

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7852 AN: 67942

Other (OTH) AF: 0.131 AC: 275 AN: 2104

Alfa AF: 0.119 Hom.: 5481

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
PhyloP100		0.76

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: rs718880; hg19: chr7-38361999;