rs11920719

Variant summary

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

The NM_015028.4(TNIK):​c.2121-5893T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0604 in 152,318 control chromosomes in the GnomAD database, including 742 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 0.060 ( 742 hom., cov: 33)

Consequence

TNIK
NM_015028.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0960
Variant links:
Genes affected
TNIK (HGNC:30765): (TRAF2 and NCK interacting kinase) Wnt signaling plays important roles in carcinogenesis and embryonic development. The protein encoded by this gene is a serine/threonine kinase that functions as an activator of the Wnt signaling pathway. Mutations in this gene are associated with an autosomal recessive form of cognitive disability. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2017]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TNIKNM_015028.4 linkuse as main transcriptc.2121-5893T>G intron_variant ENST00000436636.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TNIKENST00000436636.7 linkuse as main transcriptc.2121-5893T>G intron_variant 1 NM_015028.4 A1Q9UKE5-1

Frequencies

GnomAD3 genomes
AF:
0.0603
AC:
9173
AN:
152200
Hom.:
741
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.182
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0634
Gnomad ASJ
AF:
0.00376
Gnomad EAS
AF:
0.0406
Gnomad SAS
AF:
0.0463
Gnomad FIN
AF:
0.00678
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00106
Gnomad OTH
AF:
0.0430
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0604
AC:
9199
AN:
152318
Hom.:
742
Cov.:
33
AF XY:
0.0592
AC XY:
4411
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.182
Gnomad4 AMR
AF:
0.0634
Gnomad4 ASJ
AF:
0.00376
Gnomad4 EAS
AF:
0.0403
Gnomad4 SAS
AF:
0.0457
Gnomad4 FIN
AF:
0.00678
Gnomad4 NFE
AF:
0.00106
Gnomad4 OTH
AF:
0.0425
Alfa
AF:
0.0111
Hom.:
54
Bravo
AF:
0.0699
Asia WGS
AF:
0.0540
AC:
188
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.2
DANN
Benign
0.55

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: rs11920719; hg19: chr3-170834559; API