dbSNP rs2233278: TNIP1:n.-74C>G (chr5-151087628-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000714530.1(TNIP1):n.-74C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 152,264 control chromosomes in the GnomAD database, including 265 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 0.051 ( 265 hom., cov: 32)

Exomes 𝑓: 0.025 ( 0 hom. )

Consequence

TNIP1
ENST00000714530.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.07

Publications

32 publications found

Variant links:

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

TNIP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNIP1	NM_001252390.2 link	c.-74C>G		5_prime_UTR_variant	Exon 1 of 18		NP_001239319.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
TNIP1	ENST00000714530.1 link	n.-74C>G	non_coding_transcript_exon_variant	Exon 1 of 19		ENSP00000519775.1
TNIP1	ENST00000522226.5 link	c.-74C>G	5_prime_UTR_variant	Exon 1 of 18	2	ENSP00000428187.1
TNIP1	ENST00000714530.1 link	n.-74C>G	5_prime_UTR_variant	Exon 1 of 19		ENSP00000519775.1
TNIP1	ENST00000521001.2 link	c.-37+5810C>G	intron_variant	Intron 1 of 17	4	ENSP00000428404.2

Frequencies

GnomAD3 genomes

AF:

0.0508

AC:

7724

AN:

152106

Hom.:

264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0157

Gnomad AMI

AF:

0.0822

Gnomad AMR

AF:

0.0409

Gnomad ASJ

AF:

0.0876

Gnomad EAS

AF:

0.0936

Gnomad SAS

AF:

0.144

Gnomad FIN

AF:

0.0648

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0596

Gnomad OTH

AF:

0.0636

GnomAD4 exome

AF:

0.0250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0333

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0313

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0507

AC:

7719

AN:

152224

Hom.:

265

Cov.:

AF XY:

0.0531

AC XY:

3955

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0156

AC:

650

AN:

41544

American (AMR)

AF:

0.0409

AC:

626

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0876

AC:

304

AN:

3470

East Asian (EAS)

AF:

0.0928

AC:

479

AN:

5160

South Asian (SAS)

AF:

0.142

AC:

686

AN:

4816

European-Finnish (FIN)

AF:

0.0648

AC:

687

AN:

10602

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0596

AC:

4054

AN:

68016

Other (OTH)

AF:

0.0662

AC:

140

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

379

758

1136

1515

1894

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

288

384

480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0566

Hom.:

Bravo

AF:

0.0451

Asia WGS

AF:

0.196

AC:

680

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.59

PhyloP100

2.1

PromoterAI

-0.0080

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over