Genetic Variant TRAF3IP1:p.Thr23Thr (chr2-238320731-C-A) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. Variant got -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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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

GnomAD3 exomes

AF:

0.725

AC:

72412

AN:

99838

Hom.:

26737

AF XY:

0.724

AC XY:

39707

AN XY:

54856

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 SAS exome

AF:

0.698

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

Gnomad4 AFR exome

AF:

0.735

Gnomad4 AMR exome

AF:

0.709

Gnomad4 ASJ exome

AF:

0.779

Gnomad4 EAS exome

AF:

0.475

Gnomad4 SAS exome

AF:

0.695

Gnomad4 FIN exome

AF:

0.834

Gnomad4 NFE exome

AF:

0.715

Gnomad4 OTH exome

AF:

0.712

GnomAD4 genome

AF:

0.723

AC:

109295

AN:

151168

Hom.:

39699

Cov.:

AF XY:

0.724

AC XY:

53489

AN XY:

73862

show subpopulations

Gnomad4 AFR

AF:

0.729

Gnomad4 AMR

AF:

0.703

Gnomad4 ASJ

AF:

0.789

Gnomad4 EAS

AF:

0.475

Gnomad4 SAS

AF:

0.682

Gnomad4 FIN

AF:

0.844

Gnomad4 NFE

AF:

0.724

Gnomad4 OTH

AF:

0.738

Alfa

AF:

0.719

Hom.:

16347

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

DANN

Benign

0.93

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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