Variant chr13-50013004-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000378182.4(TRIM13):c.1064G>C(p.Ser355Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.016 in 1,613,786 control chromosomes in the GnomAD database, including 351 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.028 ( 107 hom., cov: 31)

Exomes 𝑓: 0.015 ( 244 hom. )

Consequence

TRIM13
ENST00000378182.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.956

Variant links:

Genes affected

TRIM13 (HGNC:9976): (tripartite motif containing 13) This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This gene is located on chromosome 13 within the minimal deletion region for B-cell chronic lymphocytic leukemia. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

TRIM13 links:

DLEU2 (HGNC:):

DLEU2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002144307).

BP6

Variant 13-50013004-G-C is Benign according to our data. Variant chr13-50013004-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2338675.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM13	NM_213590.3 linkuse as main transcript	c.1064G>C	p.Ser355Thr	missense_variant	2/2	ENST00000378182.4	NP_998755.1	O60858-1A0A024RDU3L7MTJ6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM13	ENST00000378182.4 linkuse as main transcript	c.1064G>C	p.Ser355Thr	missense_variant	2/2	1	NM_213590.3	ENSP00000367424.3		O60858-1

Frequencies

GnomAD3 genomes

AF:

0.0278

AC:

4223

AN:

151920

Hom.:

104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0655

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0226

Gnomad ASJ

AF:

0.0228

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00477

Gnomad FIN

AF:

0.0106

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0131

Gnomad OTH

AF:

0.0287

GnomAD3 exomes

AF:

0.0163

AC:

4092

AN:

250748

Hom.:

AF XY:

0.0149

AC XY:

2013

AN XY:

135532

show subpopulations

Gnomad AFR exome

AF:

0.0646

Gnomad AMR exome

AF:

0.0150

Gnomad ASJ exome

AF:

0.0216

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00455

Gnomad FIN exome

AF:

0.0126

Gnomad NFE exome

AF:

0.0156

Gnomad OTH exome

AF:

0.0213

GnomAD4 exome

AF:

0.0148

AC:

21595

AN:

1461748

Hom.:

244

Cov.:

AF XY:

0.0143

AC XY:

10364

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.0671

Gnomad4 AMR exome

AF:

0.0156

Gnomad4 ASJ exome

AF:

0.0222

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00589

Gnomad4 FIN exome

AF:

0.0145

Gnomad4 NFE exome

AF:

0.0141

Gnomad4 OTH exome

AF:

0.0179

GnomAD4 genome

AF:

0.0280

AC:

4250

AN:

152038

Hom.:

107

Cov.:

AF XY:

0.0275

AC XY:

2047

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.0659

Gnomad4 AMR

AF:

0.0226

Gnomad4 ASJ

AF:

0.0228

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00498

Gnomad4 FIN

AF:

0.0106

Gnomad4 NFE

AF:

0.0131

Gnomad4 OTH

AF:

0.0284

Alfa

AF:

0.0160

Hom.:

Bravo

AF:

0.0309

TwinsUK

AF:

0.0156

AC:

ALSPAC

AF:

0.0140

AC:

ESP6500AA

AF:

0.0647

AC:

285

ESP6500EA

AF:

0.0150

AC:

129

ExAC

AF:

0.0176

AC:

2142

Asia WGS

AF:

0.0100

AC:

AN:

3478

EpiCase

AF:

0.0155

EpiControl

AF:

0.0144

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 21, 2022

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.078

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.79

DEOGEN2

Benign

0.11

T;T;.;T

Eigen

Benign

-0.82

Eigen_PC

Benign

-0.74

FATHMM_MKL

Benign

0.48

LIST_S2

Benign

0.39

.;.;T;T

MetaRNN

Benign

0.0021

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.69

N;N;.;N

MutationTaster

Benign

1.0

N;N;N;N;N

PrimateAI

Benign

0.36

PROVEAN

Benign

-0.42

N;N;N;N

REVEL

Benign

0.015

Sift

Benign

0.21

T;T;T;T

Sift4G

Benign

0.63

T;T;T;T

Polyphen

0.016

B;B;B;B

Vest4

0.038

MPC

0.096

ClinPred

0.0033

GERP RS

3.1

Varity_R

0.031

gMVP

0.32

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