rs3820998

Variant names:

• chr2-161138615-C-A
• rs3820998
• ENST00000259075.6:c.-50+1552C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-161138615-C-A
• chr2-161138615-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000259075.6(TANK):​c.-50+1552C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,128 control chromosomes in the GnomAD database, including 1,730 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 (1730 hom., cov: 32)
• Consequence: TANK ENST00000259075.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232
• Publications: 5 publications found

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANK	NM_004180.3	c.-50+1552C>A		intron_variant	Intron 1 of 7		NP_004171.2
TANK	NM_133484.2	c.-50+1552C>A		intron_variant	Intron 1 of 3		NP_597841.1
TANK-AS1	NR_187173.1	n.231+20550G>T		intron_variant	Intron 2 of 2
TANK	XM_047441820.1	c.-104+1552C>A		intron_variant	Intron 1 of 8		XP_047297776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANK	ENST00000259075.6	c.-50+1552C>A		intron_variant	Intron 1 of 7	1		ENSP00000259075.2
TANK	ENST00000432002.5	c.-50+1552C>A		intron_variant	Intron 1 of 5	5		ENSP00000398157.1
TANK-AS1	ENST00000425470.1	n.165+20550G>T		intron_variant	Intron 2 of 2	3
TANK	ENST00000463502.1	n.98+1552C>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17410 AN: 152010 Hom.: 1712 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0780

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0857

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.115 AC: 17481 AN: 152128 Hom.: 1730 Cov.: 32 AF XY: 0.117 AC XY: 8672 AN XY: 74382

African (AFR) AF: 0.259 AC: 10724 AN: 41448

American (AMR) AF: 0.0780 AC: 1192 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3470

East Asian (EAS) AF: 0.191 AC: 991 AN: 5176

South Asian (SAS) AF: 0.0862 AC: 416 AN: 4826

European-Finnish (FIN) AF: 0.104 AC: 1106 AN: 10602

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0385 AC: 2619 AN: 68006

Other (OTH) AF: 0.0959 AC: 203 AN: 2116

Alfa AF: 0.0424 Hom.: 73

Bravo AF: 0.120

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		-0.23
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: rs3820998; hg19: chr2-161995126;