Variant 8-125430484-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_025195.4(TRIB1):c.-419C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 163,086 control chromosomes in the GnomAD database, including 6,311 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 0.25 ( 5790 hom., cov: 33)

Exomes 𝑓: 0.28 ( 521 hom. )

Consequence

TRIB1
NM_025195.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.26

Variant links:

Genes affected

TRIB1 (HGNC:16891): (tribbles pseudokinase 1) Enables mitogen-activated protein kinase kinase binding activity and protein kinase inhibitor activity. Involved in several processes, including JNK cascade; negative regulation of lipopolysaccharide-mediated signaling pathway; and regulation of protein kinase activity. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TRIB1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIB1	NM_025195.4 linkuse as main transcript	c.-419C>T		5_prime_UTR_variant	1/3	ENST00000311922.4	NP_079471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIB1	ENST00000311922.4 linkuse as main transcript	c.-419C>T		5_prime_UTR_variant	1/3	1	NM_025195.4	ENSP00000312150	P1	Q96RU8-1

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37777

AN:

152050

Hom.:

5789

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0665

Gnomad AMI

AF:

0.266

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.371

Gnomad FIN

AF:

0.348

Gnomad MID

AF:

0.296

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.275

GnomAD4 exome

AF:

0.280

AC:

3057

AN:

10918

Hom.:

521

Cov.:

AF XY:

0.290

AC XY:

1681

AN XY:

5788

show subpopulations

Gnomad4 AFR exome

AF:

0.0605

Gnomad4 AMR exome

AF:

0.211

Gnomad4 ASJ exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.154

Gnomad4 SAS exome

AF:

0.362

Gnomad4 FIN exome

AF:

0.305

Gnomad4 NFE exome

AF:

0.289

Gnomad4 OTH exome

AF:

0.281

GnomAD4 genome

AF:

0.248

AC:

37771

AN:

152168

Hom.:

5790

Cov.:

AF XY:

0.252

AC XY:

18756

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.0664

Gnomad4 AMR

AF:

0.265

Gnomad4 ASJ

AF:

0.347

Gnomad4 EAS

AF:

0.174

Gnomad4 SAS

AF:

0.371

Gnomad4 FIN

AF:

0.348

Gnomad4 NFE

AF:

0.331

Gnomad4 OTH

AF:

0.270

Alfa

AF:

0.294

Hom.:

1734

Bravo

AF:

0.229

Asia WGS

AF:

0.249

AC:

863

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.91

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over