17-1293747-A-G

Variant names:

• chr17-1293747-A-G
• rs12939286
• NM_172367.3:c.388-1744A>G

Variant summary

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

The NM_172367.3(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 NM_172367.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRARG1	NM_172367.3	c.388-1744A>G		intron_variant	Intron 1 of 2	ENST00000333813.4	NP_758955.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRARG1	ENST00000333813.4	c.388-1744A>G		intron_variant	Intron 1 of 2	1	NM_172367.3	ENSP00000329548.3

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

African (AFR) AF: 0.616 AC: 25488 AN: 41394

American (AMR) AF: 0.470 AC: 7158 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1708 AN: 3462

East Asian (EAS) AF: 0.444 AC: 2291 AN: 5156

South Asian (SAS) AF: 0.329 AC: 1588 AN: 4822

European-Finnish (FIN) AF: 0.462 AC: 4849 AN: 10504

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.399 AC: 27083 AN: 67930

Other (OTH) AF: 0.452 AC: 951 AN: 2106

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
PhyloP100		-0.25
Mutation Taster		=100/0	polymorphism (auto)

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: rs12939286; hg19: chr17-1197041;