chr2-161159320-G-A

Position:

• chr2-161159320-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600

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

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TANK-AS1	XR_923528.3	n.141+812C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TANK	ENST00000259075.6	c.-49-20294G>A		intron_variant		1		ENSP00000259075	P1
TANK-AS1	ENST00000425470.1	n.94-84C>T		intron_variant, non_coding_transcript_variant		3
TANK	ENST00000432002.5	c.-49-20294G>A		intron_variant		5		ENSP00000398157
TANK	ENST00000463502.1	n.99-20294G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47001 AN: 151828 Hom.: 8597 Cov.: 32

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.: 32 AF XY: 0.306 AC XY: 22722 AN XY: 74266

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.00695

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.309

Alfa AF: 0.383 Hom.: 3614

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
DANN	Benign	0.33

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

LitVar

Other links and lift over

dbSNP: rs1559526; hg19: chr2-162015831;