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

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006058.5(TNIP1):​c.358-141C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TNIP1 NM_006058.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006058.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNIP1	NM_006058.5	MANE Select	c.358-141C>A		intron	N/A	NP_006049.3
	TNIP1	NM_001437741.1		c.358-141C>A		intron	N/A	NP_001424670.1
	TNIP1	NM_001252390.2		c.358-141C>A		intron	N/A	NP_001239319.1	Q15025-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNIP1	ENST00000521591.6	TSL:1 MANE Select	c.358-141C>A		intron	N/A	ENSP00000430760.1	Q15025-1
	TNIP1	ENST00000315050.11	TSL:1	c.358-141C>A		intron	N/A	ENSP00000317891.7	Q15025-1
	TNIP1	ENST00000518977.5	TSL:1	c.358-141C>A		intron	N/A	ENSP00000430971.1	Q15025-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 554444 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 291916

African (AFR) AF: 0.00 AC: 0 AN: 15506

American (AMR) AF: 0.00 AC: 0 AN: 29480

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16502

East Asian (EAS) AF: 0.00 AC: 0 AN: 31420

South Asian (SAS) AF: 0.00 AC: 0 AN: 55240

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34996

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3920

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 337514

Other (OTH) AF: 0.00 AC: 0 AN: 29866

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.4
DANN	Benign	0.75
PhyloP100		2.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2233287; hg19: chr5-150440097;