Genetic Variant TRIM47:c.1276+14C>T (chr17-75875386-G-A) – 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.1276+14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,611,722 control chromosomes in the GnomAD database, including 30,589 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 0.22 ( 4003 hom., cov: 31)

Exomes 𝑓: 0.19 ( 26586 hom. )

Consequence

TRIM47
NM_033452.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.592

Publications

39 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:

Genome browser will be placed here

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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM47	NM_033452.3	MANE Select	c.1276+14C>T		intron	N/A	NP_258411.2	Q96LD4-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TRIM47	ENST00000254816.6	TSL:1 MANE Select	c.1276+14C>T	intron	N/A	ENSP00000254816.1	Q96LD4-1
TRIM47	ENST00000587339.2	TSL:1	n.*579+14C>T	intron	N/A	ENSP00000465010.2	A0A0M3HER3
TRIM47	ENST00000964611.1		c.1273+14C>T	intron	N/A	ENSP00000634670.1

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33118

AN:

151756

Hom.:

3990

Cov.:

show subpopulations

Gnomad AFR

AF:

0.319

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.231

GnomAD2 exomes

AF:

0.185

AC:

46469

AN:

251062

AF XY:

0.186

show subpopulations

Gnomad AFR exome

AF:

0.329

Gnomad AMR exome

AF:

0.163

Gnomad ASJ exome

AF:

0.202

Gnomad EAS exome

AF:

0.130

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.186

Gnomad OTH exome

AF:

0.199

GnomAD4 exome

AF:

0.187

AC:

273286

AN:

1459848

Hom.:

26586

Cov.:

AF XY:

0.188

AC XY:

136621

AN XY:

726324

show subpopulations

African (AFR)

AF:

0.328

AC:

10969

AN:

33428

American (AMR)

AF:

0.166

AC:

7424

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.207

AC:

5400

AN:

26132

East Asian (EAS)

AF:

0.141

AC:

5590

AN:

39690

South Asian (SAS)

AF:

0.201

AC:

17316

AN:

86218

European-Finnish (FIN)

AF:

0.121

AC:

6461

AN:

53324

Middle Eastern (MID)

AF:

0.249

AC:

1434

AN:

5764

European-Non Finnish (NFE)

AF:

0.186

AC:

206650

AN:

1110242

Other (OTH)

AF:

0.200

AC:

12042

AN:

60328

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

10139

20278

30417

40556

50695

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7366

14732

22098

29464

36830

<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:

0.218

AC:

33171

AN:

151874

Hom.:

4003

Cov.:

AF XY:

0.214

AC XY:

15887

AN XY:

74238

show subpopulations

African (AFR)

AF:

0.319

AC:

13221

AN:

41412

American (AMR)

AF:

0.187

AC:

2853

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.207

AC:

717

AN:

3468

East Asian (EAS)

AF:

0.134

AC:

692

AN:

5146

South Asian (SAS)

AF:

0.196

AC:

942

AN:

4806

European-Finnish (FIN)

AF:

0.110

AC:

1159

AN:

10584

Middle Eastern (MID)

AF:

0.229

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.190

AC:

12909

AN:

67864

Other (OTH)

AF:

0.237

AC:

499

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1266

2533

3799

5066

6332

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.205

Hom.:

6348

Bravo

AF:

0.228

Asia WGS

AF:

0.191

AC:

664

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.2

(source)

DANN

Benign

0.57

PhyloP100

0.59

PromoterAI

-0.013

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over