17-1293747-A-G

Position:

• chr17-1293747-A-G

Variant summary

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

The ENST00000333813.4(TRARG1):​c.388-1744A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,790 control chromosomes in the GnomAD database, including 17,621 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 0.47 (17621 hom., cov: 30)
• Consequence: TRARG1 ENST00000333813.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

Genes affected

TRARG1 (HGNC:29592): (trafficking regulator of GLUT4 (SLC2A4) 1) Predicted to be involved in endosome to plasma membrane protein transport and glucose import in response to insulin stimulus. Predicted to act upstream of or within vesicle fusion to plasma membrane. Predicted to be located in cytoplasmic vesicle membrane and plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRARG1	NM_172367.3	c.388-1744A>G		intron_variant		ENST00000333813.4	NP_758955.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRARG1	ENST00000333813.4	c.388-1744A>G		intron_variant		1	NM_172367.3	ENSP00000329548	P1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71547 AN: 151674 Hom.: 17597 Cov.: 30

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.454

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.472 AC: 71627 AN: 151790 Hom.: 17621 Cov.: 30 AF XY: 0.473 AC XY: 35069 AN XY: 74164

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.452

Alfa AF: 0.442 Hom.: 1903

Bravo AF: 0.480

Asia WGS AF: 0.422 AC: 1468 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.64
DANN	Benign	0.25

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: rs12939286; hg19: chr17-1197041;