Variant 3-49829151-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_005879.3(TRAIP):c.1362A>C(p.Thr454=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,614,094 control chromosomes in the GnomAD database, including 23,566 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2804 hom., cov: 32)

Exomes 𝑓: 0.16 ( 20762 hom. )

Consequence

TRAIP
NM_005879.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.72

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 3-49829151-T-G is Benign according to our data. Variant chr3-49829151-T-G is described in ClinVar as [Benign]. Clinvar id is 1098863.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.72 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TRAIP	NM_005879.3 linkuse as main transcript	c.1362A>C	p.Thr454=	synonymous_variant	15/15	ENST00000331456.7
TRAIP	XM_017005526.2 linkuse as main transcript	c.1065A>C	p.Thr355=	synonymous_variant	12/12
TRAIP	XM_047447240.1 linkuse as main transcript	c.834A>C	p.Thr278=	synonymous_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
TRAIP	ENST00000331456.7 linkuse as main transcript	c.1362A>C	p.Thr454=	synonymous_variant	15/15	1	NM_005879.3	P1
TRAIP	ENST00000491060.1 linkuse as main transcript	n.516A>C		non_coding_transcript_exon_variant	2/2	3
TRAIP	ENST00000473195.5 linkuse as main transcript	c.*535A>C		3_prime_UTR_variant, NMD_transcript_variant	10/10	3

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27315

AN:

152106

Hom.:

2790

Cov.:

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.00846

Gnomad SAS

AF:

0.0562

Gnomad FIN

AF:

0.0893

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.191

GnomAD3 exomes

AF:

0.136

AC:

34264

AN:

251294

Hom.:

2945

AF XY:

0.135

AC XY:

18302

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.261

Gnomad AMR exome

AF:

0.0885

Gnomad ASJ exome

AF:

0.156

Gnomad EAS exome

AF:

0.00500

Gnomad SAS exome

AF:

0.0565

Gnomad FIN exome

AF:

0.0905

Gnomad NFE exome

AF:

0.182

Gnomad OTH exome

AF:

0.157

GnomAD4 exome

AF:

0.162

AC:

236292

AN:

1461870

Hom.:

20762

Cov.:

AF XY:

0.159

AC XY:

115427

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.263

Gnomad4 AMR exome

AF:

0.0941

Gnomad4 ASJ exome

AF:

0.154

Gnomad4 EAS exome

AF:

0.00252

Gnomad4 SAS exome

AF:

0.0569

Gnomad4 FIN exome

AF:

0.0996

Gnomad4 NFE exome

AF:

0.178

Gnomad4 OTH exome

AF:

0.164

GnomAD4 genome

AF:

0.180

AC:

27351

AN:

152224

Hom.:

2804

Cov.:

AF XY:

0.173

AC XY:

12882

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.259

Gnomad4 AMR

AF:

0.141

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.00829

Gnomad4 SAS

AF:

0.0559

Gnomad4 FIN

AF:

0.0893

Gnomad4 NFE

AF:

0.176

Gnomad4 OTH

AF:

0.189

Alfa

AF:

0.163

Hom.:

1153

Bravo

AF:

0.189

Asia WGS

AF:

0.0530

AC:

185

AN:

3478

EpiCase

AF:

0.183

EpiControl

AF:

0.188

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 05, 2021	- -

Seckel syndrome 9

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

May 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.3

DANN

Benign

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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