Variant chr3-49828959-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005879.3(TRAIP):c.*144G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 1,148,112 control chromosomes in the GnomAD database, including 126,967 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 18255 hom., cov: 32)

Exomes 𝑓: 0.46 ( 108712 hom. )

Consequence

TRAIP
NM_005879.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.280

Variant links:

Genes affected

TRAIP (HGNC:30764): (TRAF interacting protein) This gene encodes a protein that contains an N-terminal RING finger motif and a putative coiled-coil domain. A similar murine protein interacts with TNFR-associated factor 1 (TRAF1), TNFR-associated factor 2 (TRAF2), and cylindromatosis. The interaction with TRAF2 inhibits TRAF2-mediated nuclear factor kappa-B, subunit 1 activation that is required for cell activation and protection against apoptosis. [provided by RefSeq, Jul 2008]

TRAIP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 3-49828959-C-T is Benign according to our data. Variant chr3-49828959-C-T is described in ClinVar as [Benign]. Clinvar id is 1271112.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
TRAIP	NM_005879.3 linkuse as main transcript	c.*144G>A	3_prime_UTR_variant	15/15	ENST00000331456.7
TRAIP	XM_017005526.2 linkuse as main transcript	c.*144G>A	3_prime_UTR_variant	12/12
TRAIP	XM_047447240.1 linkuse as main transcript	c.*144G>A	3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAIP	ENST00000331456.7 linkuse as main transcript	c.*144G>A		3_prime_UTR_variant	15/15	1	NM_005879.3	P1
TRAIP	ENST00000491060.1 linkuse as main transcript	n.708G>A		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes

AF:

0.477

AC:

72565

AN:

151996

Hom.:

18231

Cov.:

show subpopulations

Gnomad AFR

AF:

0.588

Gnomad AMI

AF:

0.607

Gnomad AMR

AF:

0.372

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.173

Gnomad SAS

AF:

0.380

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.489

Gnomad OTH

AF:

0.479

GnomAD4 exome

AF:

0.460

AC:

458080

AN:

995998

Hom.:

108712

Cov.:

AF XY:

0.458

AC XY:

231433

AN XY:

505202

show subpopulations

Gnomad4 AFR exome

AF:

0.588

Gnomad4 AMR exome

AF:

0.283

Gnomad4 ASJ exome

AF:

0.389

Gnomad4 EAS exome

AF:

0.205

Gnomad4 SAS exome

AF:

0.372

Gnomad4 FIN exome

AF:

0.346

Gnomad4 NFE exome

AF:

0.495

Gnomad4 OTH exome

AF:

0.455

GnomAD4 genome

AF:

0.477

AC:

72630

AN:

152114

Hom.:

18255

Cov.:

AF XY:

0.466

AC XY:

34677

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.588

Gnomad4 AMR

AF:

0.372

Gnomad4 ASJ

AF:

0.386

Gnomad4 EAS

AF:

0.172

Gnomad4 SAS

AF:

0.380

Gnomad4 FIN

AF:

0.333

Gnomad4 NFE

AF:

0.490

Gnomad4 OTH

AF:

0.483

Alfa

AF:

0.499

Hom.:

2385

Bravo

AF:

0.486

Asia WGS

AF:

0.379

AC:

1318

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.82

DANN

Benign

0.37

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over