rs13398676

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_015650.4(TRAF3IP1):c.69C>A(p.Thr23Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 1,446,688 control chromosomes in the GnomAD database, including 372,651 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T23T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.72 ( 39699 hom., cov: 33)

Exomes 𝑓: 0.71 ( 332952 hom. )

Consequence

TRAF3IP1
NM_015650.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.609

Publications

20 publications found

Variant links:

Genes affected

TRAF3IP1 (HGNC:17861): (TRAF3 interacting protein 1) The protein encoded by this gene interacts with TNF receptor-associated factor 3, tethering it to cytoskeletal microtubules. The encoded protein is also an inhibitor of the innate type I IFN response. Defects in this gene are a cause of Senior-Loken syndrome 9. [provided by RefSeq, Mar 2017]

TRAF3IP1 Gene-Disease associations (from GenCC):

Senior-Loken syndrome 9
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
Senior-Loken syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
short rib-polydactyly syndrome, Majewski type
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

TRAF3IP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP6

Variant 2-238320731-C-A is Benign according to our data. Variant chr2-238320731-C-A is described in ClinVar as [Benign]. Clinvar id is 1168003.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.609 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAF3IP1	NM_015650.4 link	c.69C>A	p.Thr23Thr	synonymous_variant	Exon 1 of 17	ENST00000373327.5	NP_056465.2	Q8TDR0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TRAF3IP1	ENST00000373327.5 link	c.69C>A	p.Thr23Thr	synonymous_variant	Exon 1 of 17	1	NM_015650.4	ENSP00000362424.4	Q8TDR0-1
TRAF3IP1	ENST00000391993.7 link	c.69C>A	p.Thr23Thr	synonymous_variant	Exon 1 of 15	1		ENSP00000375851.3	Q8TDR0-2
TRAF3IP1	ENST00000409739.2 link	n.69C>A		non_coding_transcript_exon_variant	Exon 1 of 5	3		ENSP00000386648.2	H7BZ10

Frequencies

GnomAD3 genomes

AF:

0.723

AC:

109206

AN:

151060

Hom.:

39660

Cov.:

show subpopulations

Gnomad AFR

AF:

0.729

Gnomad AMI

AF:

0.665

Gnomad AMR

AF:

0.702

Gnomad ASJ

AF:

0.789

Gnomad EAS

AF:

0.476

Gnomad SAS

AF:

0.681

Gnomad FIN

AF:

0.844

Gnomad MID

AF:

0.787

Gnomad NFE

AF:

0.724

Gnomad OTH

AF:

0.737

GnomAD2 exomes

AF:

0.725

AC:

72412

AN:

99838

AF XY:

0.724

show subpopulations

Gnomad AFR exome

AF:

0.701

Gnomad AMR exome

AF:

0.711

Gnomad ASJ exome

AF:

0.783

Gnomad EAS exome

AF:

0.441

Gnomad FIN exome

AF:

0.842

Gnomad NFE exome

AF:

0.719

Gnomad OTH exome

AF:

0.719

GnomAD4 exome

AF:

0.715

AC:

925850

AN:

1295520

Hom.:

332952

Cov.:

AF XY:

0.716

AC XY:

457730

AN XY:

639182

show subpopulations

African (AFR)

AF:

0.735

AC:

19225

AN:

26152

American (AMR)

AF:

0.709

AC:

19137

AN:

26994

Ashkenazi Jewish (ASJ)

AF:

0.779

AC:

16963

AN:

21776

East Asian (EAS)

AF:

0.475

AC:

12681

AN:

26708

South Asian (SAS)

AF:

0.695

AC:

49346

AN:

70994

European-Finnish (FIN)

AF:

0.834

AC:

37779

AN:

45290

Middle Eastern (MID)

AF:

0.837

AC:

4306

AN:

5146

European-Non Finnish (NFE)

AF:

0.715

AC:

729648

AN:

1020812

Other (OTH)

AF:

0.712

AC:

36765

AN:

51648

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

13506

27012

40517

54023

67529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.723

AC:

109295

AN:

151168

Hom.:

39699

Cov.:

AF XY:

0.724

AC XY:

53489

AN XY:

73862

show subpopulations

African (AFR)

AF:

0.729

AC:

30210

AN:

41432

American (AMR)

AF:

0.703

AC:

10670

AN:

15188

Ashkenazi Jewish (ASJ)

AF:

0.789

AC:

2730

AN:

3458

East Asian (EAS)

AF:

0.475

AC:

2426

AN:

5108

South Asian (SAS)

AF:

0.682

AC:

3290

AN:

4824

European-Finnish (FIN)

AF:

0.844

AC:

8651

AN:

10244

Middle Eastern (MID)

AF:

0.777

AC:

227

AN:

292

European-Non Finnish (NFE)

AF:

0.724

AC:

48937

AN:

67614

Other (OTH)

AF:

0.738

AC:

1549

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

1636

3273

4909

6546

8182

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.715

Hom.:

22626

Bravo

AF:

0.716

Asia WGS

AF:

0.616

AC:

1961

AN:

3176

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Nov 12, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Senior-Loken syndrome 9

Benign:1

Sep 10, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

(source)

DANN

Benign

0.93

PhyloP100

-0.61

PromoterAI

-0.11

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs13398676

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over