chr14-51058755-A-G

Position:

• chr14-51058755-A-G

Variant summary

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

The NM_001387360.1(TRIM9):​c.823-33395T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,152 control chromosomes in the GnomAD database, including 7,366 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 0.30 (7366 hom., cov: 33)
• Consequence: TRIM9 NM_001387360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

Genes affected

TRIM9 (HGNC:16288): (tripartite motif containing 9) 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. Its function has not been identified. Alternate splicing of this gene generates two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM9	NM_001387360.1	c.823-33395T>C		intron_variant		ENST00000684578.1	NP_001374289.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM9	ENST00000684578.1	c.823-33395T>C		intron_variant			NM_001387360.1	ENSP00000507131
TRIM9	ENST00000298355.7	c.823-33395T>C		intron_variant		1		ENSP00000298355	P1
TRIM9	ENST00000360392.4	c.823-33395T>C		intron_variant		1		ENSP00000353561
TRIM9	ENST00000338969.9	c.823-33395T>C		intron_variant		2		ENSP00000342970

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45463 AN: 152034 Hom.: 7346 Cov.: 33

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.299 AC: 45527 AN: 152152 Hom.: 7366 Cov.: 33 AF XY: 0.296 AC XY: 22047 AN XY: 74384

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.290

Alfa AF: 0.274 Hom.: 2973

Bravo AF: 0.311

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.52

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: rs8006348; hg19: chr14-51525473;