rs3744017

chr17-75875386-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.592

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]

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM47	NM_033452.3	c.1276+14C>T		intron_variant		ENST00000254816.6
TRIM47	XM_005257787.5	c.562+14C>T		intron_variant
TRIM47	XM_005257788.6	c.562+14C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM47	ENST00000254816.6	c.1276+14C>T		intron_variant		1	NM_033452.3	P1
TRIM47	ENST00000587339.2	c.*579+14C>T		intron_variant, NMD_transcript_variant		1
TRIM47	ENST00000592942.1	n.192+14C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33118 AN: 151756 Hom.: 3990 Cov.: 31

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

GnomAD3 exomes AF: 0.185 AC: 46469 AN: 251062 Hom.: 4604 AF XY: 0.186 AC XY: 25296 AN XY: 135770

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 SAS exome AF: 0.205

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.: 33 AF XY: 0.188 AC XY: 136621 AN XY: 726324

Gnomad4 AFR exome AF: 0.328

Gnomad4 AMR exome AF: 0.166

Gnomad4 ASJ exome AF: 0.207

Gnomad4 EAS exome AF: 0.141

Gnomad4 SAS exome AF: 0.201

Gnomad4 FIN exome AF: 0.121

Gnomad4 NFE exome AF: 0.186

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.218 AC: 33171 AN: 151874 Hom.: 4003 Cov.: 31 AF XY: 0.214 AC XY: 15887 AN XY: 74238

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.237

Alfa AF: 0.202 Hom.: 4468

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
Dann	Benign	0.57
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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

Other links and lift over

dbSNP: rs3744017; hg19: chr17-73871467;