1-228413937-T-C

Variant names:

• chr1-228413937-T-C
• rs472594
• NM_016102.4:c.430-45A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ENSG00000231563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRIM17	NM_016102.4	c.430-45A>G		intron_variant	Intron 2 of 6	ENST00000366698.7	NP_057186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM17	ENST00000366698.7	c.430-45A>G		intron_variant	Intron 2 of 6	1	NM_016102.4	ENSP00000355659.2

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

GnomAD2 exomes AF: 0.314 AC: 78100 AN: 249016 AF XY: 0.295

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 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

African (AFR) AF: 0.773 AC: 24675 AN: 31906

American (AMR) AF: 0.391 AC: 17372 AN: 44478

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 6910 AN: 25444

East Asian (EAS) AF: 0.476 AC: 18685 AN: 39272

South Asian (SAS) AF: 0.237 AC: 19918 AN: 84168

European-Finnish (FIN) AF: 0.280 AC: 14840 AN: 53076

Middle Eastern (MID) AF: 0.341 AC: 1911 AN: 5596

European-Non Finnish (NFE) AF: 0.219 AC: 223040 AN: 1020588

Other (OTH) AF: 0.282 AC: 16088 AN: 57036

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

African (AFR) AF: 0.753 AC: 31269 AN: 41524

American (AMR) AF: 0.338 AC: 5170 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3468

East Asian (EAS) AF: 0.465 AC: 2401 AN: 5158

South Asian (SAS) AF: 0.243 AC: 1176 AN: 4830

European-Finnish (FIN) AF: 0.273 AC: 2890 AN: 10600

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15132 AN: 67986

Other (OTH) AF: 0.353 AC: 747 AN: 2116

Alfa AF: 0.257 Hom.: 11920

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
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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