rs7120209

Positions:

• chr11-5612459-A-G

Variant summary

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

The NM_001003818.3(TRIM6):​c.*1117A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,088 control chromosomes in the GnomAD database, including 2,118 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 0.17 (2118 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TRIM6 NM_001003818.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

Genes affected

TRIM6 (HGNC:16277): (tripartite motif containing 6) 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, B-box type 1 and B-box type 2 domain, and a coiled-coil region. The protein localizes to the nucleus, but its specific function has not been identified. This gene is mapped to chromosome 11p15, where it resides within a TRIM gene cluster. Alternative splicing results in multiple transcript variants. A read-through transcript from this gene into the downstream TRIM34 gene has also been observed, which results in a fusion product from these neighboring family members. [provided by RefSeq, Oct 2010]

TRIM6-TRIM34 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM6	NM_001003818.3	c.*1117A>G		3_prime_UTR_variant	8/8	ENST00000380097.8
TRIM6-TRIM34	NM_001003819.4	c.985+1898A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM6	ENST00000380097.8	c.*1117A>G		3_prime_UTR_variant	8/8	1	NM_001003818.3

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25241 AN: 151970 Hom.: 2113 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.166

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.166 AC: 25270 AN: 152088 Hom.: 2118 Cov.: 32 AF XY: 0.168 AC XY: 12516 AN XY: 74352

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.170

Alfa AF: 0.162 Hom.: 724

Bravo AF: 0.162

Asia WGS AF: 0.236 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs7120209; hg19: chr11-5633689;