NM_006058.5:c.358-141C>T

Variant names:

• chr5-151060536-G-A
• rs2233287
• NM_006058.5:c.358-141C>T

Variant summary

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

The NM_006058.5(TNIP1):​c.358-141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0887 in 706,374 control chromosomes in the GnomAD database, including 3,373 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 0.11 (1103 hom., cov: 32)
  • Exomes 𝑓: 0.083 (2270 hom.)
• Consequence: TNIP1 NM_006058.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNIP1	NM_006058.5	c.358-141C>T		intron_variant	Intron 4 of 17	ENST00000521591.6	NP_006049.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNIP1	ENST00000521591.6	c.358-141C>T		intron_variant	Intron 4 of 17	1	NM_006058.5	ENSP00000430760.1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16828 AN: 152122 Hom.: 1102 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.112

GnomAD4 exome AF: 0.0827 AC: 45833 AN: 554132 Hom.: 2270 AF XY: 0.0809 AC XY: 23603 AN XY: 291752

Gnomad4 AFR exome AF: 0.192

Gnomad4 AMR exome AF: 0.0718

Gnomad4 ASJ exome AF: 0.121

Gnomad4 EAS exome AF: 0.000732

Gnomad4 SAS exome AF: 0.0523

Gnomad4 FIN exome AF: 0.0669

Gnomad4 NFE exome AF: 0.0896

Gnomad4 OTH exome AF: 0.0945

GnomAD4 genome AF: 0.111 AC: 16845 AN: 152242 Hom.: 1103 Cov.: 32 AF XY: 0.107 AC XY: 7977 AN XY: 74438

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.0913

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0392

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0925 Hom.: 1545

Bravo AF: 0.115

Asia WGS AF: 0.0350 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.6
DANN	Benign	0.73

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

Other links and lift over

dbSNP: rs2233287; hg19: chr5-150440097;