16-69057315-C-T

Variant names:

• chr16-69057315-C-T
• rs11075704
• NM_024562.2:c.3108+16894C>T

Variant summary

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

The NM_024562.2(TANGO6):​c.3108+16894C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,936 control chromosomes in the GnomAD database, including 28,592 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 0.61 (28592 hom., cov: 31)
• Consequence: TANGO6 NM_024562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 10 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANGO6	NM_024562.2	c.3108+16894C>T		intron_variant	Intron 17 of 17	ENST00000261778.2	NP_078838.1
TANGO6	XM_047434633.1	c.1695+16894C>T		intron_variant	Intron 11 of 11		XP_047290589.1
TANGO6	XM_047434634.1	c.1695+16894C>T		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.3108+16894C>T		intron_variant	Intron 17 of 17	1	NM_024562.2	ENSP00000261778.1
TANGO6	ENST00000561931.1	n.223+16894C>T		intron_variant	Intron 2 of 2	3
TANGO6	ENST00000562000.5	n.511+16894C>T		intron_variant	Intron 4 of 4	4
TANGO6	ENST00000568361.5	n.563+16894C>T		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92571 AN: 151818 Hom.: 28540 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.610 AC: 92679 AN: 151936 Hom.: 28592 Cov.: 31 AF XY: 0.609 AC XY: 45174 AN XY: 74228

African (AFR) AF: 0.533 AC: 22083 AN: 41432

American (AMR) AF: 0.669 AC: 10191 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2199 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3081 AN: 5164

South Asian (SAS) AF: 0.597 AC: 2877 AN: 4818

European-Finnish (FIN) AF: 0.587 AC: 6187 AN: 10534

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44028 AN: 67958

Other (OTH) AF: 0.637 AC: 1344 AN: 2110

Alfa AF: 0.638 Hom.: 69578

Bravo AF: 0.614

Asia WGS AF: 0.655 AC: 2276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.64
PhyloP100		0.34
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: rs11075704; hg19: chr16-69091218;