Genetic Variant TANK:c.327+3060G>T (chr2-161207853-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001199135.3(TANK):c.327+3060G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 985,160 control chromosomes in the GnomAD database, including 1,657 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 0.068 ( 1158 hom., cov: 32)

Exomes 𝑓: 0.0060 ( 499 hom. )

Consequence

TANK
NM_001199135.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.455

Publications

2 publications found

Variant links:

Genes affected

TANK (HGNC:11562): (TRAF family member associated NFKB activator) The TRAF (tumor necrosis factor receptor-associated factor) family of proteins associate with and transduce signals from members of the tumor necrosis factor receptor superfamily. The protein encoded by this gene is found in the cytoplasm and can bind to TRAF1, TRAF2, or TRAF3, thereby inhibiting TRAF function by sequestering the TRAFs in a latent state in the cytoplasm. For example, the protein encoded by this gene can block TRAF2 binding to LMP1, the Epstein-Barr virus transforming protein, and inhibit LMP1-mediated NF-kappa-B activation. Three alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]

TANK links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199135.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANK	NM_001199135.3	MANE Select	c.327+3060G>T		intron	N/A	NP_001186064.1	Q92844-1
	TANK	NM_004180.3		c.327+3060G>T		intron	N/A	NP_004171.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TANK	ENST00000392749.7	TSL:1 MANE Select	c.327+3060G>T	intron	N/A	ENSP00000376505.2	Q92844-1
TANK	ENST00000259075.6	TSL:1	c.327+3060G>T	intron	N/A	ENSP00000259075.2	Q92844-1
TANK	ENST00000468831.5	TSL:1	n.507+3060G>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0676

AC:

10277

AN:

152080

Hom.:

1145

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0295

Gnomad ASJ

AF:

0.0412

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00113

Gnomad OTH

AF:

0.0493

GnomAD4 exome

AF:

0.00599

AC:

4988

AN:

832962

Hom.:

499

Cov.:

AF XY:

0.00571

AC XY:

2195

AN XY:

384674

show subpopulations

African (AFR)

AF:

0.246

AC:

3885

AN:

15764

American (AMR)

AF:

0.0203

AC:

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.0505

AC:

260

AN:

5148

East Asian (EAS)

AF:

0.00

AC:

AN:

3626

South Asian (SAS)

AF:

0.000182

AC:

AN:

16460

European-Finnish (FIN)

AF:

0.00

AC:

AN:

276

Middle Eastern (MID)

AF:

0.0124

AC:

AN:

1618

European-Non Finnish (NFE)

AF:

0.000517

AC:

394

AN:

761790

Other (OTH)

AF:

0.0149

AC:

406

AN:

27296

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

183

366

549

732

915

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

198

396

594

792

990

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0679

AC:

10330

AN:

152198

Hom.:

1158

Cov.:

AF XY:

0.0652

AC XY:

4849

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.230

AC:

9546

AN:

41476

American (AMR)

AF:

0.0294

AC:

450

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0412

AC:

143

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5190

South Asian (SAS)

AF:

0.000622

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00113

AC:

AN:

68018

Other (OTH)

AF:

0.0488

AC:

103

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

406

812

1217

1623

2029

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

288

384

480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0315

Hom.:

1032

Bravo

AF:

0.0783

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.8

(source)

DANN

Benign

0.62

PhyloP100

-0.46

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over