dbSNP rs1559526: TANK:c.-49-20294G>A (chr2-161159320-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000259075.6(TANK):c.-49-20294G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,946 control chromosomes in the GnomAD database, including 8,599 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 0.31 ( 8599 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

TANK
ENST00000259075.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.600

Publications

5 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:

TANK-AS1 (HGNC:40575): (TANK antisense RNA 1)

TANK-AS1 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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
TANK	NM_004180.3 link	c.-49-20294G>A	intron_variant	Intron 1 of 7	NP_004171.2
TANK	NM_133484.2 link	c.-49-20294G>A	intron_variant	Intron 1 of 3	NP_597841.1
TANK-AS1	NR_187173.1 link	n.160-84C>T	intron_variant	Intron 1 of 2
TANK	XM_047441820.1 link	c.-103-17792G>A	intron_variant	Intron 1 of 8	XP_047297776.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
TANK	ENST00000259075.6 link	c.-49-20294G>A	intron_variant	Intron 1 of 7	1	ENSP00000259075.2
TANK	ENST00000432002.5 link	c.-49-20294G>A	intron_variant	Intron 1 of 5	5	ENSP00000398157.1
TANK-AS1	ENST00000425470.1 link	n.94-84C>T	intron_variant	Intron 1 of 2	3
TANK	ENST00000463502.1 link	n.99-20294G>A	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.310

AC:

47001

AN:

151828

Hom.:

8597

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.417

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.00674

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.303

Gnomad NFE

AF:

0.412

Gnomad OTH

AF:

0.313

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

GnomAD4 genome

AF:

0.309

AC:

47017

AN:

151946

Hom.:

8599

Cov.:

AF XY:

0.306

AC XY:

22722

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.140

AC:

5801

AN:

41450

American (AMR)

AF:

0.417

AC:

6367

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.313

AC:

1084

AN:

3466

East Asian (EAS)

AF:

0.00695

AC:

AN:

5182

South Asian (SAS)

AF:

0.280

AC:

1346

AN:

4812

European-Finnish (FIN)

AF:

0.317

AC:

3339

AN:

10530

Middle Eastern (MID)

AF:

0.305

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.412

AC:

28004

AN:

67940

Other (OTH)

AF:

0.309

AC:

652

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1543

3087

4630

6174

7717

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

462

924

1386

1848

2310

<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:

0.379

Hom.:

4396

Bravo

AF:

0.309

Asia WGS

AF:

0.117

AC:

406

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.55

(source)

DANN

Benign

0.33

PhyloP100

-0.60

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over