rs10186736

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000392749.7(TANK):​c.327+3060G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 985,160 control chromosomes in the GnomAD database, including 1,657 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 0.068 ( 1158 hom., cov: 32)
Exomes 𝑓: 0.0060 ( 499 hom. )

Consequence

TANK
ENST00000392749.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.455
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TANKNM_001199135.3 linkuse as main transcriptc.327+3060G>T intron_variant ENST00000392749.7 NP_001186064.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TANKENST00000392749.7 linkuse as main transcriptc.327+3060G>T intron_variant 1 NM_001199135.3 ENSP00000376505 P1Q92844-1

Frequencies

GnomAD3 genomes
AF:
0.0676
AC:
10277
AN:
152080
Hom.:
1145
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.230
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0295
Gnomad ASJ
AF:
0.0412
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.00113
Gnomad OTH
AF:
0.0493
GnomAD4 exome
AF:
0.00599
AC:
4988
AN:
832962
Hom.:
499
Cov.:
30
AF XY:
0.00571
AC XY:
2195
AN XY:
384674
show subpopulations
Gnomad4 AFR exome
AF:
0.246
Gnomad4 AMR exome
AF:
0.0203
Gnomad4 ASJ exome
AF:
0.0505
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000182
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000517
Gnomad4 OTH exome
AF:
0.0149
GnomAD4 genome
AF:
0.0679
AC:
10330
AN:
152198
Hom.:
1158
Cov.:
32
AF XY:
0.0652
AC XY:
4849
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.230
Gnomad4 AMR
AF:
0.0294
Gnomad4 ASJ
AF:
0.0412
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00113
Gnomad4 OTH
AF:
0.0488
Alfa
AF:
0.0126
Hom.:
188
Bravo
AF:
0.0783
Asia WGS
AF:
0.0140
AC:
48
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
5.8
DANN
Benign
0.62

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10186736; hg19: chr2-162064364; API