Genetic Variant TRIM47:c.676-54T>C (chr17-75876867-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033452.3(TRIM47):c.676-54T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 1,572,576 control chromosomes in the GnomAD database, including 87,330 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 0.42 ( 16675 hom., cov: 33)

Exomes 𝑓: 0.31 ( 70655 hom. )

Consequence

TRIM47
NM_033452.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

Publications

47 publications found

Variant links:

Genes affected

TRIM47 (HGNC:19020): (tripartite motif containing 47) Enables ubiquitin-protein transferase activity. Involved in protein ubiquitination. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

TRIM47 links:

ENSG00000267801 (HGNC:):

ENSG00000267801 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033452.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM47	NM_033452.3	MANE Select	c.676-54T>C		intron	N/A	NP_258411.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TRIM47	ENST00000254816.6	TSL:1 MANE Select	c.676-54T>C	intron	N/A	ENSP00000254816.1
TRIM47	ENST00000587339.2	TSL:1	n.345-54T>C	intron	N/A	ENSP00000465010.2
ENSG00000267801	ENST00000586076.1	TSL:6	n.496A>G	non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.417

AC:

63458

AN:

152046

Hom.:

16614

Cov.:

show subpopulations

Gnomad AFR

AF:

0.750

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.296

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.225

Gnomad SAS

AF:

0.320

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.399

GnomAD4 exome

AF:

0.305

AC:

433553

AN:

1420412

Hom.:

70655

Cov.:

AF XY:

0.306

AC XY:

215742

AN XY:

705786

show subpopulations

African (AFR)

AF:

0.765

AC:

25055

AN:

32746

American (AMR)

AF:

0.240

AC:

10442

AN:

43452

Ashkenazi Jewish (ASJ)

AF:

0.348

AC:

8892

AN:

25588

East Asian (EAS)

AF:

0.263

AC:

10266

AN:

38990

South Asian (SAS)

AF:

0.333

AC:

28221

AN:

84722

European-Finnish (FIN)

AF:

0.225

AC:

11239

AN:

50032

Middle Eastern (MID)

AF:

0.359

AC:

1891

AN:

5264

European-Non Finnish (NFE)

AF:

0.294

AC:

318281

AN:

1080804

Other (OTH)

AF:

0.328

AC:

19266

AN:

58814

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

14616

29232

43847

58463

73079

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10702

21404

32106

42808

53510

<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:

0.418

AC:

63574

AN:

152164

Hom.:

16675

Cov.:

AF XY:

0.409

AC XY:

30413

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.750

AC:

31149

AN:

41508

American (AMR)

AF:

0.295

AC:

4515

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.347

AC:

1204

AN:

3470

East Asian (EAS)

AF:

0.225

AC:

1166

AN:

5176

South Asian (SAS)

AF:

0.321

AC:

1552

AN:

4828

European-Finnish (FIN)

AF:

0.225

AC:

2382

AN:

10596

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.300

AC:

20400

AN:

67976

Other (OTH)

AF:

0.405

AC:

856

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1643

3285

4928

6570

8213

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

544

1088

1632

2176

2720

<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:

0.337

Hom.:

11430

Bravo

AF:

0.437

Asia WGS

AF:

0.332

AC:

1156

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.15

(source)

DANN

Benign

0.58

PhyloP100

-1.4

PromoterAI

-0.0013

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

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