Variant 5-151033641-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The ENST00000521591.6(TNIP1):c.1746G>A(p.Pro582=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 718,746 control chromosomes in the GnomAD database, including 93 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.013 ( 9 hom., cov: 27)

Exomes 𝑓: 0.020 ( 84 hom. )

Consequence

TNIP1
ENST00000521591.6 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.28

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 5-151033641-C-T is Benign according to our data. Variant chr5-151033641-C-T is described in ClinVar as [Benign]. Clinvar id is 775226.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0134 (1424/106224) while in subpopulation AMR AF= 0.0214 (226/10570). AF 95% confidence interval is 0.0191. There are 9 homozygotes in gnomad4. There are 672 alleles in male gnomad4 subpopulation. Median coverage is 27. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNIP1	NM_006058.5 linkuse as main transcript	c.1746G>A	p.Pro582=	synonymous_variant	16/18	ENST00000521591.6	NP_006049.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNIP1	ENST00000521591.6 linkuse as main transcript	c.1746G>A	p.Pro582=	synonymous_variant	16/18	1	NM_006058.5	ENSP00000430760	P3	Q15025-1

Frequencies

GnomAD3 genomes

AF:

0.0134

AC:

1425

AN:

106170

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00322

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.0214

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00422

Gnomad FIN

AF:

0.0114

Gnomad MID

AF:

0.0217

Gnomad NFE

AF:

0.0170

Gnomad OTH

AF:

0.0146

GnomAD3 exomes

AF:

0.00936

AC:

1064

AN:

113694

Hom.:

AF XY:

0.0102

AC XY:

640

AN XY:

62588

show subpopulations

Gnomad AFR exome

AF:

0.00213

Gnomad AMR exome

AF:

0.00601

Gnomad ASJ exome

AF:

0.0115

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00305

Gnomad FIN exome

AF:

0.00607

Gnomad NFE exome

AF:

0.0140

Gnomad OTH exome

AF:

0.00758

GnomAD4 exome

AF:

0.0200

AC:

12230

AN:

612522

Hom.:

Cov.:

AF XY:

0.0198

AC XY:

5864

AN XY:

295790

show subpopulations

Gnomad4 AFR exome

AF:

0.00493

Gnomad4 AMR exome

AF:

0.0119

Gnomad4 ASJ exome

AF:

0.0200

Gnomad4 EAS exome

AF:

0.000137

Gnomad4 SAS exome

AF:

0.00545

Gnomad4 FIN exome

AF:

0.0111

Gnomad4 NFE exome

AF:

0.0222

Gnomad4 OTH exome

AF:

0.0201

GnomAD4 genome

AF:

0.0134

AC:

1424

AN:

106224

Hom.:

Cov.:

AF XY:

0.0132

AC XY:

672

AN XY:

51102

show subpopulations

Gnomad4 AFR

AF:

0.00321

Gnomad4 AMR

AF:

0.0214

Gnomad4 ASJ

AF:

0.0150

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00423

Gnomad4 FIN

AF:

0.0114

Gnomad4 NFE

AF:

0.0170

Gnomad4 OTH

AF:

0.0144

Alfa

AF:

0.00962

Hom.:

Bravo

AF:

0.0108

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

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

1.1

DANN

Benign

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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