rs7708392

Variant names:

• chr5-151077924-G-C
• rs7708392
• NM_006058.5:c.-37+2956C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006058.5(TNIP1):​c.-37+2956C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,074 control chromosomes in the GnomAD database, including 18,419 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 0.44 (18419 hom., cov: 32)
• Consequence: TNIP1 NM_006058.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 70 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNIP1	NM_006058.5	c.-37+2956C>G		intron_variant	Intron 1 of 17	ENST00000521591.6	NP_006049.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNIP1	ENST00000521591.6	c.-37+2956C>G		intron_variant	Intron 1 of 17	1	NM_006058.5	ENSP00000430760.1

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66349 AN: 151956 Hom.: 18375 Cov.: 32

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.437 AC: 66452 AN: 152074 Hom.: 18419 Cov.: 32 AF XY: 0.441 AC XY: 32768 AN XY: 74360

African (AFR) AF: 0.764 AC: 31663 AN: 41452

American (AMR) AF: 0.431 AC: 6577 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3472

East Asian (EAS) AF: 0.730 AC: 3775 AN: 5170

South Asian (SAS) AF: 0.420 AC: 2030 AN: 4828

European-Finnish (FIN) AF: 0.286 AC: 3022 AN: 10568

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17060 AN: 67992

Other (OTH) AF: 0.397 AC: 840 AN: 2114

Alfa AF: 0.348 Hom.: 1511

Bravo AF: 0.465

Asia WGS AF: 0.549 AC: 1908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	11
DANN	Benign	0.37
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7708392; hg19: chr5-150457485;