NM_001199135.3:c.100-181G>A

Variant names:

• chr2-161203306-G-A
• rs1267075
• NM_001199135.3:c.100-181G>A

Variant summary

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

The NM_001199135.3(TANK):​c.100-181G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,128 control chromosomes in the GnomAD database, including 51,313 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 0.82 (51313 hom., cov: 32)
• Consequence: TANK NM_001199135.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 8 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199135.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANK	NM_001199135.3	MANE Select	c.100-181G>A		intron	N/A	NP_001186064.1
	TANK	NM_004180.3		c.100-181G>A		intron	N/A	NP_004171.2
	TANK	NM_133484.2		c.100-181G>A		intron	N/A	NP_597841.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANK	ENST00000392749.7	TSL:1 MANE Select	c.100-181G>A		intron	N/A	ENSP00000376505.2
	TANK	ENST00000259075.6	TSL:1	c.100-181G>A		intron	N/A	ENSP00000259075.2
	TANK	ENST00000403609.1	TSL:1	c.100-181G>A		intron	N/A	ENSP00000385983.1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124640 AN: 152010 Hom.: 51260 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.820 AC: 124750 AN: 152128 Hom.: 51313 Cov.: 32 AF XY: 0.824 AC XY: 61242 AN XY: 74354

African (AFR) AF: 0.762 AC: 31625 AN: 41500

American (AMR) AF: 0.869 AC: 13293 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2796 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5167 AN: 5188

South Asian (SAS) AF: 0.856 AC: 4131 AN: 4826

European-Finnish (FIN) AF: 0.800 AC: 8458 AN: 10568

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56582 AN: 67962

Other (OTH) AF: 0.818 AC: 1727 AN: 2110

Alfa AF: 0.833 Hom.: 144846

Bravo AF: 0.825

Asia WGS AF: 0.919 AC: 3192 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		0.072
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: rs1267075; hg19: chr2-162059817;