Genetic Variant TNIP1:c.*926A>G (chr5-151029787-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006058.5(TNIP1):c.*926A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,924 control chromosomes in the GnomAD database, including 24,515 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 0.56 ( 24515 hom., cov: 30)

Consequence

TNIP1
NM_006058.5 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.45

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNIP1	NM_006058.5 link	c.*926A>G		downstream_gene_variant		ENST00000521591.6	NP_006049.3	Q15025-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNIP1	ENST00000521591.6 link	c.*926A>G		downstream_gene_variant		1	NM_006058.5	ENSP00000430760.1		Q15025-1

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

85050

AN:

151806

Hom.:

24497

Cov.:

show subpopulations

Gnomad AFR

AF:

0.457

Gnomad AMI

AF:

0.523

Gnomad AMR

AF:

0.594

Gnomad ASJ

AF:

0.547

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.399

Gnomad FIN

AF:

0.613

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.637

Gnomad OTH

AF:

0.546

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

GnomAD4 genome

AF:

0.560

AC:

85099

AN:

151924

Hom.:

24515

Cov.:

AF XY:

0.556

AC XY:

41281

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.457

Gnomad4 AMR

AF:

0.594

Gnomad4 ASJ

AF:

0.547

Gnomad4 EAS

AF:

0.348

Gnomad4 SAS

AF:

0.400

Gnomad4 FIN

AF:

0.613

Gnomad4 NFE

AF:

0.637

Gnomad4 OTH

AF:

0.547

Alfa

AF:

0.577

Hom.:

3783

Bravo

AF:

0.555

Asia WGS

AF:

0.403

AC:

1398

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.16

DANN

Benign

0.37

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over