rs472594

Positions:

• chr1-228413937-T-C
• chr1-228413937-T-G

Variant summary

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

The NM_016102.4(TRIM17):​c.430-45A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,513,748 control chromosomes in the GnomAD database, including 66,061 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 0.40 (15872 hom., cov: 33)
  • Exomes 𝑓: 0.25 (50189 hom.)
• Consequence: TRIM17 NM_016102.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

Genes affected

TRIM17 (HGNC:13430): (tripartite motif containing 17) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to cytoplasmic bodies. The protein is expressed almost exclusively in the testis, but its function is unknown. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM17	NM_016102.4	c.430-45A>G		intron_variant		ENST00000366698.7	NP_057186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM17	ENST00000366698.7	c.430-45A>G		intron_variant		1	NM_016102.4	ENSP00000355659	P1
	ENST00000701501.1	n.283+6459T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60013 AN: 152066 Hom.: 15827 Cov.: 33

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.353

GnomAD3 exomes AF: 0.314 AC: 78100 AN: 249016 Hom.: 14929 AF XY: 0.295 AC XY: 39811 AN XY: 134754

Gnomad AFR exome AF: 0.762

Gnomad AMR exome AF: 0.405

Gnomad ASJ exome AF: 0.272

Gnomad EAS exome AF: 0.476

Gnomad SAS exome AF: 0.237

Gnomad FIN exome AF: 0.278

Gnomad NFE exome AF: 0.229

Gnomad OTH exome AF: 0.275

GnomAD4 exome AF: 0.252 AC: 343439 AN: 1361564 Hom.: 50189 Cov.: 21 AF XY: 0.249 AC XY: 170306 AN XY: 682778

Gnomad4 AFR exome AF: 0.773

Gnomad4 AMR exome AF: 0.391

Gnomad4 ASJ exome AF: 0.272

Gnomad4 EAS exome AF: 0.476

Gnomad4 SAS exome AF: 0.237

Gnomad4 FIN exome AF: 0.280

Gnomad4 NFE exome AF: 0.219

Gnomad4 OTH exome AF: 0.282

GnomAD4 genome AF: 0.395 AC: 60116 AN: 152184 Hom.: 15872 Cov.: 33 AF XY: 0.394 AC XY: 29291 AN XY: 74412

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.353

Alfa AF: 0.240 Hom.: 7329

Bravo AF: 0.422

Asia WGS AF: 0.344 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.26
DANN	Benign	0.30

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: rs472594; hg19: chr1-228601638; COSMIC: COSV54381299; COSMIC: COSV54381299;