rs11157796

chr14-51077905-C-T

Variant summary

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

The NM_001387360.1(TRIM9):c.822+16213G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,136 control chromosomes in the GnomAD database, including 3,498 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 0.21 (3498 hom., cov: 32)
• Consequence: TRIM9 NM_001387360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM9	NM_001387360.1	c.822+16213G>A		intron_variant		ENST00000684578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM9	ENST00000684578.1	c.822+16213G>A		intron_variant			NM_001387360.1
TRIM9	ENST00000298355.7	c.822+16213G>A		intron_variant		1		P1
TRIM9	ENST00000360392.4	c.822+16213G>A		intron_variant		1
TRIM9	ENST00000338969.9	c.822+16213G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31809 AN: 152018 Hom.: 3491 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0502

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.209 AC: 31846 AN: 152136 Hom.: 3498 Cov.: 32 AF XY: 0.205 AC XY: 15251 AN XY: 74366

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0501

Gnomad4 SAS AF: 0.0988

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.196

Alfa AF: 0.232 Hom.: 8626

Bravo AF: 0.202

Asia WGS AF: 0.0960 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.1
Dann	Benign	0.56

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: rs11157796; hg19: chr14-51544623;