5-151089865-C-T

Position:

• chr5-151089865-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521001.1(TNIP1):​c.-37+3573G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,944 control chromosomes in the GnomAD database, including 18,837 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 0.49 (18837 hom., cov: 33)
• Consequence: TNIP1 ENST00000521001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNIP1	ENST00000521001.1	c.-37+3573G>A		intron_variant		4		ENSP00000428404

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74741 AN: 151826 Hom.: 18801 Cov.: 33

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.492 AC: 74831 AN: 151944 Hom.: 18837 Cov.: 33 AF XY: 0.498 AC XY: 36960 AN XY: 74264

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.475

Alfa AF: 0.461 Hom.: 33884

Bravo AF: 0.502

Asia WGS AF: 0.581 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3762999; hg19: chr5-150469426;