dbSNP rs3754972: TANK:c.100-2980T>A (chr2-161200507-T-A) – 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.100-2980T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 980,758 control chromosomes in the GnomAD database, including 2,975 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 0.11 ( 1687 hom., cov: 32)

Exomes 𝑓: 0.043 ( 1288 hom. )

Consequence

TANK
NM_001199135.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.102

Publications

3 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANK	NM_001199135.3 link	c.100-2980T>A		intron_variant	Intron 2 of 7	ENST00000392749.7	NP_001186064.1	Q92844-1B2R7S3Q6NW12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANK	ENST00000392749.7 link	c.100-2980T>A		intron_variant	Intron 2 of 7	1	NM_001199135.3	ENSP00000376505.2		Q92844-1

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17226

AN:

152080

Hom.:

1669

Cov.:

show subpopulations

Gnomad AFR

AF:

0.256

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0777

Gnomad ASJ

AF:

0.0625

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.0837

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0386

Gnomad OTH

AF:

0.0911

GnomAD4 exome

AF:

0.0430

AC:

35588

AN:

828560

Hom.:

1288

Cov.:

AF XY:

0.0424

AC XY:

16217

AN XY:

382824

show subpopulations

African (AFR)

AF:

0.261

AC:

4062

AN:

15540

American (AMR)

AF:

0.0571

AC:

AN:

980

Ashkenazi Jewish (ASJ)

AF:

0.0698

AC:

358

AN:

5132

East Asian (EAS)

AF:

0.182

AC:

655

AN:

3594

South Asian (SAS)

AF:

0.0752

AC:

1228

AN:

16326

European-Finnish (FIN)

AF:

0.0580

AC:

AN:

276

Middle Eastern (MID)

AF:

0.0378

AC:

AN:

1612

European-Non Finnish (NFE)

AF:

0.0362

AC:

27472

AN:

757958

Other (OTH)

AF:

0.0619

AC:

1680

AN:

27142

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.430

Heterozygous variant carriers

1433

2867

4300

5734

7167

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.114

AC:

17297

AN:

152198

Hom.:

1687

Cov.:

AF XY:

0.115

AC XY:

8576

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.256

AC:

10630

AN:

41494

American (AMR)

AF:

0.0777

AC:

1189

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0625

AC:

217

AN:

3472

East Asian (EAS)

AF:

0.176

AC:

914

AN:

5190

South Asian (SAS)

AF:

0.0842

AC:

406

AN:

4824

European-Finnish (FIN)

AF:

0.104

AC:

1102

AN:

10586

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0386

AC:

2623

AN:

68024

Other (OTH)

AF:

0.0963

AC:

203

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

712

1424

2135

2847

3559

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0794

Hom.:

128

Bravo

AF:

0.118

Asia WGS

AF:

0.188

AC:

648

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.1

(source)

DANN

Benign

0.38

PhyloP100

0.10

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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rs3754972

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over