5-151083077-T-C

Position:

• chr5-151083077-T-C

Variant summary

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

The ENST00000315050.11(TNIP1):​c.-37+4008A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,084 control chromosomes in the GnomAD database, including 25,020 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 0.55 (25020 hom., cov: 32)
• Consequence: TNIP1 ENST00000315050.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNIP1	NM_001252390.2	c.-37+4514A>G		intron_variant			NP_001239319.1
TNIP1	NM_001252391.2	c.-37+4008A>G		intron_variant			NP_001239320.1
TNIP1	NM_001252392.2	c.-37+4008A>G		intron_variant			NP_001239321.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNIP1	ENST00000315050.11	c.-37+4008A>G		intron_variant		1		ENSP00000317891	P3
TNIP1	ENST00000523338.5	c.-37+4008A>G		intron_variant		1		ENSP00000428243
TNIP1	ENST00000521001.1	c.-37+10361A>G		intron_variant		4		ENSP00000428404

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83574 AN: 151966 Hom.: 24975 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.550 AC: 83678 AN: 152084 Hom.: 25020 Cov.: 32 AF XY: 0.552 AC XY: 41017 AN XY: 74358

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.515

Alfa AF: 0.446 Hom.: 22848

Bravo AF: 0.571

Asia WGS AF: 0.597 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.71

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: rs13168551; hg19: chr5-150462638; COSMIC: COSV59310582; COSMIC: COSV59310582;