11-5604373-A-G

Position:

• chr11-5604373-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.508-161A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,942 control chromosomes in the GnomAD database, including 15,643 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 0.45 (15643 hom., cov: 31)
• Consequence: TRIM6 NM_001003818.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM6	NM_001003818.3	c.508-161A>G		intron_variant		ENST00000380097.8
TRIM6-TRIM34	NM_001003819.4	c.508-161A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM6	ENST00000380097.8	c.508-161A>G		intron_variant		1	NM_001003818.3

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67691 AN: 151822 Hom.: 15603 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.491

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.446 AC: 67792 AN: 151942 Hom.: 15643 Cov.: 31 AF XY: 0.447 AC XY: 33232 AN XY: 74272

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.497

Alfa AF: 0.402 Hom.: 16341

Bravo AF: 0.466

Asia WGS AF: 0.611 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.99
DANN	Benign	0.42

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: rs7108470; hg19: chr11-5625603;