Genetic Variant NM_007028.5:c.849T>C (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

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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