rs1959536

chr14-50980053-T-G

Variant summary

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

The NM_001387360.1(TRIM9):c.2163-504A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0933 in 152,252 control chromosomes in the GnomAD database, including 1,629 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 0.093 (1629 hom., cov: 33)
• Consequence: TRIM9 NM_001387360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM9	NM_001387360.1	c.2163-504A>C		intron_variant		ENST00000684578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM9	ENST00000684578.1	c.2163-504A>C		intron_variant			NM_001387360.1
TRIM9	ENST00000298355.7	c.1908-504A>C		intron_variant		1		P1
TRIM9	ENST00000338969.9	c.2151-504A>C		intron_variant		2
TRIM9	ENST00000555170.1	n.513-504A>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14165 AN: 152134 Hom.: 1618 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.0310

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0631

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

GnomAD4 genome AF: 0.0933 AC: 14211 AN: 152252 Hom.: 1629 Cov.: 33 AF XY: 0.0914 AC XY: 6804 AN XY: 74464

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.0723

Gnomad4 ASJ AF: 0.00260

Gnomad4 EAS AF: 0.0314

Gnomad4 SAS AF: 0.0561

Gnomad4 FIN AF: 0.0225

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0579 Hom.: 259

Bravo AF: 0.107

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.3
Dann	Benign	0.39

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: rs1959536; hg19: chr14-51446771;