chr13-50013004-G-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_213590.3(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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.028 ( 107 hom., cov: 31)

Exomes 𝑓: 0.015 ( 244 hom. )

Consequence

TRIM13
NM_213590.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.956

Publications

13 publications found

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:13748): (deleted in lymphocytic leukemia 2) This locus represents a microRNA host gene and also produces long alternatively spliced non-coding RNAs. This genome region was observed to be deleted or epigenetically suppressed in leukemia, and was implicated as a negative regulator of cell proliferation. However, an alternative transcript produced at this locus was also found to promote progression through the cell cycle via angiotensin I converting enzyme 2 and cyclin D1. [provided by RefSeq, Dec 2017]

DLEU2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_213590.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TRIM13	NM_213590.3	MANE Select	c.1064G>C	p.Ser355Thr	missense	Exon 2 of 2	NP_998755.1	O60858-1
TRIM13	NM_001007278.3		c.1073G>C	p.Ser358Thr	missense	Exon 4 of 4	NP_001007279.1	O60858-3
TRIM13	NM_005798.5		c.1064G>C	p.Ser355Thr	missense	Exon 3 of 3	NP_005789.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TRIM13	ENST00000378182.4	TSL:1 MANE Select	c.1064G>C	p.Ser355Thr	missense	Exon 2 of 2	ENSP00000367424.3	O60858-1
TRIM13	ENST00000356017.8	TSL:1	c.1073G>C	p.Ser358Thr	missense	Exon 4 of 4	ENSP00000348299.4	O60858-3
TRIM13	ENST00000420995.6	TSL:1	c.1064G>C	p.Ser355Thr	missense	Exon 3 of 3	ENSP00000412943.2	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

GnomAD2 exomes

AF:

0.0163

AC:

4092

AN:

250748

AF XY:

0.0149

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 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

African (AFR)

AF:

0.0671

AC:

2248

AN:

33478

American (AMR)

AF:

0.0156

AC:

699

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.0222

AC:

579

AN:

26128

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39686

South Asian (SAS)

AF:

0.00589

AC:

508

AN:

86236

European-Finnish (FIN)

AF:

0.0145

AC:

772

AN:

53392

Middle Eastern (MID)

AF:

0.0137

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0141

AC:

15628

AN:

1111950

Other (OTH)

AF:

0.0179

AC:

1081

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

1228

2456

3683

4911

6139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

620

1240

1860

2480

3100

<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:

0.0280

AC:

4250

AN:

152038

Hom.:

107

Cov.:

AF XY:

0.0275

AC XY:

2047

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.0659

AC:

2731

AN:

41444

American (AMR)

AF:

0.0226

AC:

345

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.0228

AC:

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5172

South Asian (SAS)

AF:

0.00498

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0106

AC:

112

AN:

10566

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0131

AC:

892

AN:

67984

Other (OTH)

AF:

0.0284

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

207

413

620

826

1033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

176

220

<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:

0.0160

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

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.078

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Benign

0.79

DEOGEN2

Benign

0.11

Eigen

Benign

-0.82

Eigen_PC

Benign

-0.74

FATHMM_MKL

Benign

0.48

LIST_S2

Benign

0.39

MetaRNN

Benign

0.0021

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.69

PhyloP100

0.96

PrimateAI

Benign

0.36

PROVEAN

Benign

-0.42

REVEL

Benign

0.015

Sift

Benign

0.21

Sift4G

Benign

0.63

Polyphen

0.016

Vest4

0.038

MPC

0.096

ClinPred

0.0033

GERP RS

3.1

Varity_R

0.031

gMVP

0.32

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over