chr16-68927079-T-C

Variant names:

• chr16-68927079-T-C
• rs10500547
• NM_024562.2:c.2128-489T>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.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
• Publications: 8 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]

U7 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024562.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANGO6	NM_024562.2	MANE Select	c.2128-489T>C		intron	N/A	NP_078838.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANGO6	ENST00000261778.2	TSL:1 MANE Select	c.2128-489T>C		intron	N/A	ENSP00000261778.1
	TANGO6	ENST00000953309.1		c.2128-489T>C		intron	N/A	ENSP00000623368.1
	TANGO6	ENST00000953308.1		c.2224-489T>C		intron	N/A	ENSP00000623367.1

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

African (AFR) AF: 0.300 AC: 9 AN: 30

American (AMR) AF: 0.0590 AC: 34 AN: 576

Ashkenazi Jewish (ASJ) AF: 0.0962 AC: 5 AN: 52

East Asian (EAS) AF: 0.0962 AC: 5 AN: 52

South Asian (SAS) AF: 0.0726 AC: 17 AN: 234

European-Finnish (FIN) AF: 0.141 AC: 9 AN: 64

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 6

European-Non Finnish (NFE) AF: 0.124 AC: 304 AN: 2450

Other (OTH) AF: 0.117 AC: 15 AN: 128

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

African (AFR) AF: 0.260 AC: 10798 AN: 41508

American (AMR) AF: 0.126 AC: 1922 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3472

East Asian (EAS) AF: 0.0517 AC: 268 AN: 5186

South Asian (SAS) AF: 0.0990 AC: 478 AN: 4826

European-Finnish (FIN) AF: 0.163 AC: 1722 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10092 AN: 68002

Other (OTH) AF: 0.162 AC: 343 AN: 2112

Alfa AF: 0.148 Hom.: 3134

Bravo AF: 0.174

Asia WGS AF: 0.106 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.4
DANN	Benign	0.39
PhyloP100		-0.014
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: rs10500547; hg19: chr16-68960982;