Genetic Variant TRAF3IP1:c.-99delC (chr2-238320563-GC-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_015650.4(TRAF3IP1):c.-99delC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 980,564 control chromosomes in the GnomAD database, including 3,436 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.062 ( 395 hom., cov: 32)

Exomes 𝑓: 0.086 ( 3041 hom. )

Consequence

TRAF3IP1
NM_015650.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.166

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 was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 2-238320563-GC-G is Benign according to our data. Variant chr2-238320563-GC-G is described in ClinVar as [Benign]. Clinvar id is 1281208.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAF3IP1	NM_015650.4 link	c.-99delC		5_prime_UTR_variant	Exon 1 of 17	ENST00000373327.5	NP_056465.2	Q8TDR0-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TRAF3IP1	ENST00000373327.5 link	c.-99delC	5_prime_UTR_variant	Exon 1 of 17	1	NM_015650.4	ENSP00000362424.4	Q8TDR0-1
TRAF3IP1	ENST00000391993.7 link	c.-99delC	5_prime_UTR_variant	Exon 1 of 15	1		ENSP00000375851.3	Q8TDR0-2
TRAF3IP1	ENST00000409739.2 link	n.-99delC	non_coding_transcript_exon_variant	Exon 1 of 5	3		ENSP00000386648.2	H7BZ10
TRAF3IP1	ENST00000409739.2 link	n.-99delC	5_prime_UTR_variant	Exon 1 of 5	3		ENSP00000386648.2	H7BZ10

Frequencies

GnomAD3 genomes

AF:

0.0620

AC:

9340

AN:

150644

Hom.:

396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0145

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.0379

Gnomad ASJ

AF:

0.133

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0518

Gnomad FIN

AF:

0.0920

Gnomad MID

AF:

0.124

Gnomad NFE

AF:

0.0929

Gnomad OTH

AF:

0.0551

GnomAD4 exome

AF:

0.0857

AC:

71088

AN:

829816

Hom.:

3041

Cov.:

AF XY:

0.0865

AC XY:

33648

AN XY:

389146

show subpopulations

African (AFR)

AF:

0.00939

AC:

145

AN:

15438

American (AMR)

AF:

0.0503

AC:

110

AN:

2188

Ashkenazi Jewish (ASJ)

AF:

0.149

AC:

893

AN:

6002

East Asian (EAS)

AF:

0.000992

AC:

AN:

5038

South Asian (SAS)

AF:

0.0578

AC:

972

AN:

16828

European-Finnish (FIN)

AF:

0.162

AC:

1073

AN:

6604

Middle Eastern (MID)

AF:

0.0838

AC:

146

AN:

1742

European-Non Finnish (NFE)

AF:

0.0873

AC:

65265

AN:

747826

Other (OTH)

AF:

0.0881

AC:

2479

AN:

28150

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

3295

6590

9884

13179

16474

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0619

AC:

9332

AN:

150748

Hom.:

395

Cov.:

AF XY:

0.0597

AC XY:

4399

AN XY:

73658

show subpopulations

African (AFR)

AF:

0.0144

AC:

597

AN:

41368

American (AMR)

AF:

0.0378

AC:

573

AN:

15154

Ashkenazi Jewish (ASJ)

AF:

0.133

AC:

460

AN:

3450

East Asian (EAS)

AF:

0.000387

AC:

AN:

5170

South Asian (SAS)

AF:

0.0514

AC:

248

AN:

4826

European-Finnish (FIN)

AF:

0.0920

AC:

925

AN:

10056

Middle Eastern (MID)

AF:

0.120

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0929

AC:

6265

AN:

67432

Other (OTH)

AF:

0.0540

AC:

113

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

472

944

1416

1888

2360

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0444

Hom.:

Bravo

AF:

0.0543

Asia WGS

AF:

0.0290

AC:

AN:

3306

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jul 14, 2020

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.17

Mutation Taster

=300/0

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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chr2-238320563-GC-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over