rs62382331

Variant names:

• chr5-151033641-C-A
• rs62382331
• NM_006058.5:c.1746G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-151033641-C-A
• chr5-151033641-C-G
• chr5-151033641-C-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_006058.5(TNIP1):​c.1746G>T​(p.Pro582Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000979 in 612,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P582P) has been classified as Benign.

• Frequency:
  • Genomes: not found (cov: 27)
  • Exomes 𝑓: 0.0000098 (0 hom.)
• Consequence: TNIP1 NM_006058.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.28
• 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 -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP7: Synonymous conserved (PhyloP=-3.28 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNIP1	NM_006058.5	c.1746G>T	p.Pro582Pro	synonymous_variant	Exon 16 of 18	ENST00000521591.6	NP_006049.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNIP1	ENST00000521591.6	c.1746G>T	p.Pro582Pro	synonymous_variant	Exon 16 of 18	1	NM_006058.5	ENSP00000430760.1

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome AF: 0.00000979 AC: 6 AN: 612616 Hom.: 0 Cov.: 26 AF XY: 0.0000101 AC XY: 3 AN XY: 295836

African (AFR) AF: 0.00 AC: 0 AN: 12784

American (AMR) AF: 0.00 AC: 0 AN: 12404

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7354

East Asian (EAS) AF: 0.00 AC: 0 AN: 14568

South Asian (SAS) AF: 0.00 AC: 0 AN: 19644

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24658

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2472

European-Non Finnish (NFE) AF: 0.0000121 AC: 6 AN: 495356

Other (OTH) AF: 0.00 AC: 0 AN: 23376

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	0.30
DANN	Benign	0.83
PhyloP100		-3.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs62382331; hg19: chr5-150413202;