Variant 5-151049891-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006058.5(TNIP1):c.779C>T(p.Ala260Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00496 in 1,614,088 control chromosomes in the GnomAD database, including 201 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.021 ( 99 hom., cov: 32)

Exomes 𝑓: 0.0033 ( 102 hom. )

Consequence

TNIP1
NM_006058.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.726

Variant links:

Genes affected

TNIP1 (HGNC:16903): (TNFAIP3 interacting protein 1) This gene encodes an A20-binding protein which plays a role in autoimmunity and tissue homeostasis through the regulation of nuclear factor kappa-B activation. Mutations in this gene have been associated with psoriatic arthritis, rheumatoid arthritis, and systemic lupus erythematosus. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

TNIP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018417537).

BP6

Variant 5-151049891-G-A is Benign according to our data. Variant chr5-151049891-G-A is described in ClinVar as [Benign]. Clinvar id is 778221.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNIP1	NM_006058.5 linkuse as main transcript	c.779C>T	p.Ala260Val	missense_variant	8/18	ENST00000521591.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNIP1	ENST00000521591.6 linkuse as main transcript	c.779C>T	p.Ala260Val	missense_variant	8/18	1	NM_006058.5	P3	Q15025-1

Frequencies

GnomAD3 genomes

AF:

0.0207

AC:

3152

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0665

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00890

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.0204

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00538

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000823

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.00740

AC:

1860

AN:

251400

Hom.:

AF XY:

0.00605

AC XY:

822

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.0681

Gnomad AMR exome

AF:

0.00286

Gnomad ASJ exome

AF:

0.00347

Gnomad EAS exome

AF:

0.0179

Gnomad SAS exome

AF:

0.000719

Gnomad FIN exome

AF:

0.00504

Gnomad NFE exome

AF:

0.00105

Gnomad OTH exome

AF:

0.00635

GnomAD4 exome

AF:

0.00331

AC:

4845

AN:

1461838

Hom.:

102

Cov.:

AF XY:

0.00309

AC XY:

2248

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.0716

Gnomad4 AMR exome

AF:

0.00331

Gnomad4 ASJ exome

AF:

0.00295

Gnomad4 EAS exome

AF:

0.0186

Gnomad4 SAS exome

AF:

0.000869

Gnomad4 FIN exome

AF:

0.00493

Gnomad4 NFE exome

AF:

0.000618

Gnomad4 OTH exome

AF:

0.00725

GnomAD4 genome

AF:

0.0208

AC:

3166

AN:

152250

Hom.:

Cov.:

AF XY:

0.0206

AC XY:

1532

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0664

Gnomad4 AMR

AF:

0.00889

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.0204

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00538

Gnomad4 NFE

AF:

0.000823

Gnomad4 OTH

AF:

0.0166

Alfa

AF:

0.00532

Hom.:

Bravo

AF:

0.0233

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0742

AC:

327

ESP6500EA

AF:

0.000698

AC:

ExAC

AF:

0.00887

AC:

1077

Asia WGS

AF:

0.0250

AC:

AN:

3478

EpiCase

AF:

0.000491

EpiControl

AF:

0.000593

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.66

Cadd

Benign

Dann

Benign

0.97

Eigen

Benign

-0.73

Eigen_PC

Benign

-0.76

FATHMM_MKL

Benign

0.059

LIST_S2

Benign

0.72

T;T;T;.;.;.;.;T;T;.;T;T

MetaRNN

Benign

0.0018

T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

N;N;N;N;N;N;N;N;N

PrimateAI

Benign

0.26

PROVEAN

Benign

-0.87

N;N;.;N;N;.;N;N;N;N;N;N

REVEL

Benign

0.073

Sift

Benign

0.11

T;T;.;T;T;.;T;T;T;T;T;T

Sift4G

Benign

0.13

T;T;T;T;T;T;T;T;T;T;T;.

Polyphen

0.021

.;.;.;B;.;.;B;B;.;.;.;.

Vest4

0.034

MVP

0.043

MPC

0.21

ClinPred

0.0052

GERP RS

2.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.023

gMVP

0.21

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over