rs1267074

Variant names:

• chr2-161195062-T-A
• rs1267074
• NM_001199135.3:c.100-8425T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-161195062-T-A
• chr2-161195062-T-C
• chr2-161195062-T-G

Variant summary

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

The NM_001199135.3(TANK):​c.100-8425T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,128 control chromosomes in the GnomAD database, including 5,532 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 (5532 hom., cov: 32)
• Consequence: TANK NM_001199135.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• 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=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANK	NM_001199135.3	c.100-8425T>A		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.100-8425T>A		intron_variant	Intron 2 of 7	1	NM_001199135.3	ENSP00000376505.2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39664 AN: 152010 Hom.: 5534 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.261 AC: 39674 AN: 152128 Hom.: 5532 Cov.: 32 AF XY: 0.262 AC XY: 19503 AN XY: 74382

African (AFR) AF: 0.167 AC: 6940 AN: 41524

American (AMR) AF: 0.236 AC: 3607 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1202 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2050 AN: 5178

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4822

European-Finnish (FIN) AF: 0.281 AC: 2973 AN: 10582

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20728 AN: 67956

Other (OTH) AF: 0.281 AC: 594 AN: 2114

Alfa AF: 0.164 Hom.: 343

Bravo AF: 0.254

Asia WGS AF: 0.300 AC: 1041 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.1
DANN	Benign	0.89
PhyloP100		0.26
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: rs1267074; hg19: chr2-162051573;