rs72789205

chr16-69057269-G-Achr16-69057269-G-T

Variant summary

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

The NM_024562.2(TANGO6):c.3108+16848G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0732 in 151,964 control chromosomes in the GnomAD database, including 512 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 0.073 (512 hom., cov: 28)
• Consequence: TANGO6 NM_024562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TANGO6	NM_024562.2	c.3108+16848G>A		intron_variant		ENST00000261778.2
TANGO6	XM_047434633.1	c.1695+16848G>A		intron_variant
TANGO6	XM_047434634.1	c.1695+16848G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANGO6	ENST00000261778.2	c.3108+16848G>A		intron_variant		1	NM_024562.2	P1
TANGO6	ENST00000561931.1	n.223+16848G>A		intron_variant, non_coding_transcript_variant		3
TANGO6	ENST00000562000.5	n.511+16848G>A		intron_variant, non_coding_transcript_variant		4
TANGO6	ENST00000568361.5	n.563+16848G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11095 AN: 151846 Hom.: 504 Cov.: 28

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.0824

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.0907

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.0825

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

GnomAD4 genome AF: 0.0732 AC: 11131 AN: 151964 Hom.: 512 Cov.: 28 AF XY: 0.0720 AC XY: 5349 AN XY: 74284

Gnomad4 AFR AF: 0.0236

Gnomad4 AMR AF: 0.0826

Gnomad4 ASJ AF: 0.0651

Gnomad4 EAS AF: 0.0271

Gnomad4 SAS AF: 0.0830

Gnomad4 FIN AF: 0.0907

Gnomad4 NFE AF: 0.0997

Gnomad4 OTH AF: 0.0907

Alfa AF: 0.0540 Hom.: 77

Bravo AF: 0.0712

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	4.3
Dann	Benign	0.74

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: rs72789205; hg19: chr16-69091172;