5-151078585-C-T

Position:

• chr5-151078585-C-T

Variant summary

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

The NM_006058.5(TNIP1):​c.-37+2295G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,060 control chromosomes in the GnomAD database, including 18,387 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 (18387 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TNIP1 NM_006058.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• 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/exons	MANE	Protein	UniProt
TNIP1	NM_006058.5	c.-37+2295G>A		intron_variant		ENST00000521591.6	NP_006049.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNIP1	ENST00000521591.6	c.-37+2295G>A		intron_variant		1	NM_006058.5	ENSP00000430760.1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66210 AN: 151942 Hom.: 18343 Cov.: 33

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.393

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.436 AC: 66313 AN: 152060 Hom.: 18387 Cov.: 33 AF XY: 0.439 AC XY: 32647 AN XY: 74294

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.396

Alfa AF: 0.286 Hom.: 15941

Bravo AF: 0.465

Asia WGS AF: 0.548 AC: 1905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	15
DANN	Benign	0.93

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: rs10036748; hg19: chr5-150458146;