Variant rs1055129 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
TRIM47	NM_033452.3 linkuse as main transcript	c.676-54T>C	intron_variant	ENST00000254816.6	NP_258411.2
TRIM47	XM_005257787.5 linkuse as main transcript	c.-39-54T>C	intron_variant		XP_005257844.1
TRIM47	XM_005257788.6 linkuse as main transcript	c.-39-54T>C	intron_variant		XP_005257845.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM47	ENST00000254816.6 linkuse as main transcript	c.676-54T>C		intron_variant		1	NM_033452.3	ENSP00000254816	P1	Q96LD4-1
	ENST00000586076.1 linkuse as main transcript	n.496A>G		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome

AF:

0.765

Gnomad4 AMR exome

AF:

0.240

Gnomad4 ASJ exome

AF:

0.348

Gnomad4 EAS exome

AF:

0.263

Gnomad4 SAS exome

AF:

0.333

Gnomad4 FIN exome

AF:

0.225

Gnomad4 NFE exome

AF:

0.294

Gnomad4 OTH exome

AF:

0.328

GnomAD4 genome

AF:

0.418

AC:

63574

AN:

152164

Hom.:

16675

Cov.:

AF XY:

0.409

AC XY:

30413

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.750

Gnomad4 AMR

AF:

0.295

Gnomad4 ASJ

AF:

0.347

Gnomad4 EAS

AF:

0.225

Gnomad4 SAS

AF:

0.321

Gnomad4 FIN

AF:

0.225

Gnomad4 NFE

AF:

0.300

Gnomad4 OTH

AF:

0.405

Alfa

AF:

0.321

Hom.:

4211

Bravo

AF:

0.437

Asia WGS

AF:

0.332

AC:

1156

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.15

DANN

Benign

0.58

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over