rs6889239

Positions:

• chr5-151078210-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.-37+2670A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,168 control chromosomes in the GnomAD database, including 15,905 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 0.41 (15905 hom., cov: 33)
• Consequence: TNIP1 NM_006058.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNIP1	NM_006058.5	c.-37+2670A>G		intron_variant		ENST00000521591.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNIP1	ENST00000521591.6	c.-37+2670A>G		intron_variant		1	NM_006058.5	P3

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62894 AN: 152050 Hom.: 15871 Cov.: 33

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.414 AC: 62983 AN: 152168 Hom.: 15905 Cov.: 33 AF XY: 0.418 AC XY: 31097 AN XY: 74402

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.385

Alfa AF: 0.377 Hom.: 1937

Bravo AF: 0.439

Asia WGS AF: 0.544 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs6889239; hg19: chr5-150457771;