Genetic Variant TRIM31:p.His283His (chr6-30108087-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_007028.5(TRIM31):c.849T>C(p.His283His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 1,596,558 control chromosomes in the GnomAD database, including 318,077 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.65 ( 32300 hom., cov: 31)

Exomes 𝑓: 0.62 ( 285777 hom. )

Consequence

TRIM31
NM_007028.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.319

Publications

50 publications found

Variant links:

Genes affected

TRIM31 (HGNC:16289): (tripartite motif containing 31) This gene encodes a protein that functions as an E3 ubiquitin-protein ligase. This gene shows altered expression in certain tumors and may be a negative regulator of cell growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

TRIM31 links:

TRIM31-AS1 (HGNC:39761): (TRIM31 antisense RNA 1)

TRIM31-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP7

Synonymous conserved (PhyloP=0.319 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM31	NM_007028.5 link	c.849T>C	p.His283His	synonymous_variant	Exon 6 of 9	ENST00000376734.4	NP_008959.3	Q9BZY9-1Q2L6J1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM31	ENST00000376734.4 link	c.849T>C	p.His283His	synonymous_variant	Exon 6 of 9	5	NM_007028.5	ENSP00000365924.3		Q9BZY9-1

Frequencies

GnomAD3 genomes

AF:

0.648

AC:

98394

AN:

151814

Hom.:

32281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.643

Gnomad AMI

AF:

0.765

Gnomad AMR

AF:

0.692

Gnomad ASJ

AF:

0.734

Gnomad EAS

AF:

0.864

Gnomad SAS

AF:

0.853

Gnomad FIN

AF:

0.659

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.603

Gnomad OTH

AF:

0.641

GnomAD2 exomes

AF:

0.680

AC:

167501

AN:

246282

AF XY:

0.684

show subpopulations

Gnomad AFR exome

AF:

0.647

Gnomad AMR exome

AF:

0.692

Gnomad ASJ exome

AF:

0.721

Gnomad EAS exome

AF:

0.887

Gnomad FIN exome

AF:

0.657

Gnomad NFE exome

AF:

0.609

Gnomad OTH exome

AF:

0.653

GnomAD4 exome

AF:

0.623

AC:

900294

AN:

1444626

Hom.:

285777

Cov.:

AF XY:

0.630

AC XY:

452997

AN XY:

719466

show subpopulations

African (AFR)

AF:

0.636

AC:

21050

AN:

33116

American (AMR)

AF:

0.692

AC:

30899

AN:

44658

Ashkenazi Jewish (ASJ)

AF:

0.716

AC:

18653

AN:

26060

East Asian (EAS)

AF:

0.779

AC:

30882

AN:

39628

South Asian (SAS)

AF:

0.825

AC:

70978

AN:

86084

European-Finnish (FIN)

AF:

0.647

AC:

33796

AN:

52204

Middle Eastern (MID)

AF:

0.649

AC:

3724

AN:

5738

European-Non Finnish (NFE)

AF:

0.594

AC:

652092

AN:

1097246

Other (OTH)

AF:

0.638

AC:

38220

AN:

59892

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.431

Heterozygous variant carriers

14583

29166

43748

58331

72914

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17766

35532

53298

71064

88830

<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:

0.648

AC:

98464

AN:

151932

Hom.:

32300

Cov.:

AF XY:

0.656

AC XY:

48753

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.643

AC:

26585

AN:

41372

American (AMR)

AF:

0.692

AC:

10573

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.734

AC:

2546

AN:

3468

East Asian (EAS)

AF:

0.863

AC:

4462

AN:

5168

South Asian (SAS)

AF:

0.854

AC:

4113

AN:

4818

European-Finnish (FIN)

AF:

0.659

AC:

6955

AN:

10546

Middle Eastern (MID)

AF:

0.622

AC:

183

AN:

294

European-Non Finnish (NFE)

AF:

0.603

AC:

41001

AN:

67958

Other (OTH)

AF:

0.639

AC:

1350

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1786

3572

5358

7144

8930

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

794

1588

2382

3176

3970

<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:

0.620

Hom.:

126889

Bravo

AF:

0.646

Asia WGS

AF:

0.811

AC:

2821

AN:

3478

EpiCase

AF:

0.607

EpiControl

AF:

0.617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

3.1

(source)

DANN

Benign

0.94

PhyloP100

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over