16-69065765-T-C

Variant names:

• chr16-69065765-T-C
• rs9332431
• NM_024562.2:c.3109-17720T>C

Variant summary

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

The NM_024562.2(TANGO6):​c.3109-17720T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,052 control chromosomes in the GnomAD database, including 18,339 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 0.48 (18339 hom., cov: 32)
• Consequence: TANGO6 NM_024562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778
• Publications: 7 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANGO6	NM_024562.2	c.3109-17720T>C		intron_variant	Intron 17 of 17	ENST00000261778.2	NP_078838.1
TANGO6	XM_047434633.1	c.1696-17720T>C		intron_variant	Intron 11 of 11		XP_047290589.1
TANGO6	XM_047434634.1	c.1696-17720T>C		intron_variant	Intron 11 of 11		XP_047290590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANGO6	ENST00000261778.2	c.3109-17720T>C		intron_variant	Intron 17 of 17	1	NM_024562.2	ENSP00000261778.1
TANGO6	ENST00000561931.1	n.224-17720T>C		intron_variant	Intron 2 of 2	3
TANGO6	ENST00000562000.5	n.512-17720T>C		intron_variant	Intron 4 of 4	4
TANGO6	ENST00000568361.5	n.564-17720T>C		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73410 AN: 151932 Hom.: 18307 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.483 AC: 73485 AN: 152052 Hom.: 18339 Cov.: 32 AF XY: 0.482 AC XY: 35795 AN XY: 74310

African (AFR) AF: 0.353 AC: 14675 AN: 41520

American (AMR) AF: 0.564 AC: 8611 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1925 AN: 3468

East Asian (EAS) AF: 0.585 AC: 3022 AN: 5162

South Asian (SAS) AF: 0.556 AC: 2669 AN: 4804

European-Finnish (FIN) AF: 0.455 AC: 4806 AN: 10558

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36133 AN: 67966

Other (OTH) AF: 0.507 AC: 1071 AN: 2112

Alfa AF: 0.517 Hom.: 8174

Bravo AF: 0.487

Asia WGS AF: 0.595 AC: 2069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.0
DANN	Benign	0.34
PhyloP100		0.78
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: rs9332431; hg19: chr16-69099668;