ENST00000478359.5:n.*260C>G – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000478359.5(TRAF3IP3):n.*260C>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 0.374 in 737,612 control chromosomes in the GnomAD database, including 54,061 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 0.34 ( 9480 hom., cov: 33)

Exomes 𝑓: 0.38 ( 44581 hom. )

Consequence

TRAF3IP3
ENST00000478359.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233

Publications

11 publications found

Variant links:

Genes affected

TRAF3IP3 (HGNC:30766): (TRAF3 interacting protein 3) The gene encodes a protein that mediates cell growth by modulating the c-Jun N-terminal kinase signal transduction pathway. The encoded protein may also interact with a large multi-protein assembly containing the phosphatase 2A catalytic subunit. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

TRAF3IP3 links:

C1orf74 (HGNC:26319): (chromosome 1 open reading frame 74)

C1orf74 links:

ENSG00000289700 (HGNC:):

ENSG00000289700 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=-0.77).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf74	NM_152485.4 link	c.*3305G>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000294811.2	NP_689698.1	Q96LT6A0A0A8K8E6
TRAF3IP3	NM_025228.4 link	c.1312+146C>G		intron_variant	Intron 14 of 16	ENST00000367025.8	NP_079504.2	Q9Y228-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
C1orf74	ENST00000294811.2 link	c.*3305G>C	3_prime_UTR_variant	Exon 2 of 2	1	NM_152485.4	ENSP00000294811.1	Q96LT6
TRAF3IP3	ENST00000367025.8 link	c.1312+146C>G	intron_variant	Intron 14 of 16	1	NM_025228.4	ENSP00000355992.3	Q9Y228-1
ENSG00000289700	ENST00000696133.1 link	c.*4129G>C	downstream_gene_variant				ENSP00000512426.1	A0A8Q3SJ75

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51313

AN:

152018

Hom.:

9476

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.488

Gnomad EAS

AF:

0.242

Gnomad SAS

AF:

0.352

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.420

Gnomad NFE

AF:

0.419

Gnomad OTH

AF:

0.369

GnomAD4 exome

AF:

0.383

AC:

224251

AN:

585476

Hom.:

44581

Cov.:

AF XY:

0.387

AC XY:

121938

AN XY:

315458

show subpopulations

African (AFR)

AF:

0.208

AC:

3348

AN:

16122

American (AMR)

AF:

0.220

AC:

7665

AN:

34874

Ashkenazi Jewish (ASJ)

AF:

0.501

AC:

10131

AN:

20202

East Asian (EAS)

AF:

0.257

AC:

8294

AN:

32250

South Asian (SAS)

AF:

0.371

AC:

23601

AN:

63668

European-Finnish (FIN)

AF:

0.368

AC:

18193

AN:

49416

Middle Eastern (MID)

AF:

0.476

AC:

1949

AN:

4098

European-Non Finnish (NFE)

AF:

0.417

AC:

138947

AN:

333488

Other (OTH)

AF:

0.387

AC:

12123

AN:

31358

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

8229

16457

24686

32914

41143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

842

1684

2526

3368

4210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.337

AC:

51335

AN:

152136

Hom.:

9480

Cov.:

AF XY:

0.335

AC XY:

24894

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.207

AC:

8612

AN:

41512

American (AMR)

AF:

0.281

AC:

4294

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.488

AC:

1694

AN:

3468

East Asian (EAS)

AF:

0.243

AC:

1260

AN:

5178

South Asian (SAS)

AF:

0.352

AC:

1697

AN:

4826

European-Finnish (FIN)

AF:

0.381

AC:

4022

AN:

10570

Middle Eastern (MID)

AF:

0.418

AC:

122

AN:

292

European-Non Finnish (NFE)

AF:

0.419

AC:

28503

AN:

67986

Other (OTH)

AF:

0.370

AC:

781

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1692

3384

5077

6769

8461

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.379

Hom.:

1422

Bravo

AF:

0.321

Asia WGS

AF:

0.315

AC:

1094

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

7.8

(source)

DANN

Benign

0.76

PhyloP100

-0.23

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over