NM_152906.7:c.-39-4054C>T

Variant names:

• chr22-20032706-C-T
• rs2008591
• NM_152906.7:c.-39-4054C>T

Variant summary

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

The NM_152906.7(TANGO2):​c.-39-4054C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,074 control chromosomes in the GnomAD database, including 12,273 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 0.40 (12273 hom., cov: 33)
• Consequence: TANGO2 NM_152906.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 14 publications found

Genes affected

TANGO2 (HGNC:25439): (transport and golgi organization 2 homolog) This gene belongs to the transport and Golgi organization family, whose members are predicted to play roles in secretory protein loading in the endoplasmic reticulum. Depletion of this gene in Drosophila S2 cells causes fusion of the Golgi with the ER. In mouse tissue culture cells, this protein co-localizes with a mitochondrially targeted mCherry protein and displays very low levels of co-localization with Golgi and peroxisomes. Allelic variants of this gene are associated with rhabdomyolysis, metabolic crises with encephalopathy, and cardiac arrhythmia. [provided by RefSeq, Apr 2016]

TANGO2 Gene-Disease associations (from GenCC):

• recurrent metabolic encephalomyopathic crises-rhabdomyolysis-cardiac arrhythmia-intellectual disability syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152906.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANGO2	NM_152906.7	MANE Select	c.-39-4054C>T		intron	N/A	NP_690870.3
	TANGO2	NM_001322141.2		c.-156-4054C>T		intron	N/A	NP_001309070.1
	TANGO2	NM_001322142.2		c.-39-4054C>T		intron	N/A	NP_001309071.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANGO2	ENST00000327374.9	TSL:1 MANE Select	c.-39-4054C>T		intron	N/A	ENSP00000332721.4
	TANGO2	ENST00000401833.5	TSL:5	c.-156-4054C>T		intron	N/A	ENSP00000384827.1
	TANGO2	ENST00000456048.5	TSL:2	c.-156-4054C>T		intron	N/A	ENSP00000403645.2

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60087 AN: 151956 Hom.: 12279 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.395 AC: 60104 AN: 152074 Hom.: 12273 Cov.: 33 AF XY: 0.390 AC XY: 28970 AN XY: 74346

African (AFR) AF: 0.494 AC: 20508 AN: 41492

American (AMR) AF: 0.314 AC: 4804 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1602 AN: 5156

South Asian (SAS) AF: 0.277 AC: 1332 AN: 4816

European-Finnish (FIN) AF: 0.343 AC: 3634 AN: 10584

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26023 AN: 67958

Other (OTH) AF: 0.383 AC: 808 AN: 2110

Alfa AF: 0.375 Hom.: 5747

Bravo AF: 0.402

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		-0.93
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: rs2008591; hg19: chr22-20020229;