rs10500547

chr16-68927079-T-C

Variant summary

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

The NM_024562.2(TANGO6):c.2128-489T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 155,788 control chromosomes in the GnomAD database, including 2,571 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 0.17 (2539 hom., cov: 31)
  • Exomes 𝑓: 0.11 (32 hom.)
• Consequence: TANGO6 NM_024562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

Genes affected

TANGO6 (HGNC:25749): (transport and golgi organization 6 homolog) Predicted to be involved in protein secretion. Predicted to be integral component of 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TANGO6	NM_024562.2	c.2128-489T>C		intron_variant		ENST00000261778.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANGO6	ENST00000261778.2	c.2128-489T>C		intron_variant		1	NM_024562.2	P1
TANGO6	ENST00000561856.1	c.*289-489T>C		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26174 AN: 152078 Hom.: 2520 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.157

GnomAD4 exome AF: 0.111 AC: 398 AN: 3592 Hom.: 32 AF XY: 0.114 AC XY: 211 AN XY: 1846

Gnomad4 AFR exome AF: 0.300

Gnomad4 AMR exome AF: 0.0590

Gnomad4 ASJ exome AF: 0.0962

Gnomad4 EAS exome AF: 0.0962

Gnomad4 SAS exome AF: 0.0726

Gnomad4 FIN exome AF: 0.141

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.117

GnomAD4 genome AF: 0.172 AC: 26246 AN: 152196 Hom.: 2539 Cov.: 31 AF XY: 0.169 AC XY: 12611 AN XY: 74426

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0517

Gnomad4 SAS AF: 0.0990

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.162

Alfa AF: 0.144 Hom.: 2364

Bravo AF: 0.174

Asia WGS AF: 0.106 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.4
Dann	Benign	0.39

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: rs10500547; hg19: chr16-68960982;