dbSNP rs3744017: 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:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
TRIM47	NM_033452.3 link	c.1276+14C>T	intron_variant	Intron 5 of 5	ENST00000254816.6	NP_258411.2	Q96LD4-1
TRIM47	XM_005257787.5 link	c.562+14C>T	intron_variant	Intron 5 of 5		XP_005257844.1	Q96LD4-2
TRIM47	XM_005257788.6 link	c.562+14C>T	intron_variant	Intron 5 of 5		XP_005257845.1	Q96LD4-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TRIM47	ENST00000254816.6 link	c.1276+14C>T	intron_variant	Intron 5 of 5	1	NM_033452.3	ENSP00000254816.1	Q96LD4-1
TRIM47	ENST00000587339.2 link	n.*579+14C>T	intron_variant	Intron 5 of 5	1		ENSP00000465010.2	A0A0M3HER3
TRIM47	ENST00000592942.1 link	n.192+14C>T	intron_variant	Intron 1 of 1	2

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 v4.3

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

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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