rs4958881

chr5-151070675-T-C

Variant summary

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

The NM_006058.5(TNIP1):c.-36-5544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,154 control chromosomes in the GnomAD database, including 4,713 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 0.20 (4713 hom., cov: 32)
• Consequence: TNIP1 NM_006058.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.29

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNIP1	NM_006058.5	c.-36-5544A>G		intron_variant		ENST00000521591.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNIP1	ENST00000521591.6	c.-36-5544A>G		intron_variant		1	NM_006058.5	P3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30811 AN: 152036 Hom.: 4696 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.203 AC: 30861 AN: 152154 Hom.: 4713 Cov.: 32 AF XY: 0.199 AC XY: 14772 AN XY: 74392

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0619

Gnomad4 SAS AF: 0.0522

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.185

Alfa AF: 0.132 Hom.: 1482

Bravo AF: 0.216

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.032
Dann	Benign	0.54

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: rs4958881; hg19: chr5-150450236;