NM_001199135.3:c.99+11309C>T

Variant names:

• chr2-161191070-C-T
• rs1267072
• NM_001199135.3:c.99+11309C>T

Variant summary

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

The NM_001199135.3(TANK):​c.99+11309C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,062 control chromosomes in the GnomAD database, including 5,692 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 0.26 (5692 hom., cov: 32)
• Consequence: TANK NM_001199135.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 6 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANK	NM_001199135.3	c.99+11309C>T		intron_variant	Intron 2 of 7	ENST00000392749.7	NP_001186064.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANK	ENST00000392749.7	c.99+11309C>T		intron_variant	Intron 2 of 7	1	NM_001199135.3	ENSP00000376505.2

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40222 AN: 151944 Hom.: 5693 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.265 AC: 40234 AN: 152062 Hom.: 5692 Cov.: 32 AF XY: 0.267 AC XY: 19820 AN XY: 74332

African (AFR) AF: 0.168 AC: 6971 AN: 41476

American (AMR) AF: 0.246 AC: 3752 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1215 AN: 3466

East Asian (EAS) AF: 0.395 AC: 2044 AN: 5170

South Asian (SAS) AF: 0.239 AC: 1154 AN: 4828

European-Finnish (FIN) AF: 0.302 AC: 3196 AN: 10578

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.307 AC: 20884 AN: 67948

Other (OTH) AF: 0.279 AC: 590 AN: 2112

Alfa AF: 0.294 Hom.: 3507

Bravo AF: 0.257

Asia WGS AF: 0.302 AC: 1052 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.63
DANN	Benign	0.30
PhyloP100		-0.10
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: rs1267072; hg19: chr2-162047581;