14-50980053-T-G

Variant names:

• chr14-50980053-T-G
• rs1959536
• NM_001387360.1:c.2163-504A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387360.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM9	NM_001387360.1	MANE Select	c.2163-504A>C		intron	N/A	NP_001374289.1
	TRIM9	NM_001387361.1		c.2151-504A>C		intron	N/A	NP_001374290.1
	TRIM9	NM_001387362.1		c.2139-504A>C		intron	N/A	NP_001374291.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM9	ENST00000684578.1	MANE Select	c.2163-504A>C		intron	N/A	ENSP00000507131.1
	TRIM9	ENST00000298355.7	TSL:1	c.1908-504A>C		intron	N/A	ENSP00000298355.3
	TRIM9	ENST00000338969.9	TSL:2	c.2151-504A>C		intron	N/A	ENSP00000342970.5

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

African (AFR) AF: 0.273 AC: 11316 AN: 41504

American (AMR) AF: 0.0723 AC: 1105 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00260 AC: 9 AN: 3468

East Asian (EAS) AF: 0.0314 AC: 163 AN: 5186

South Asian (SAS) AF: 0.0561 AC: 271 AN: 4828

European-Finnish (FIN) AF: 0.0225 AC: 239 AN: 10626

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0141 AC: 957 AN: 68026

Other (OTH) AF: 0.0634 AC: 134 AN: 2114

Alfa AF: 0.0519 Hom.: 449

Bravo AF: 0.107

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1959536; hg19: chr14-51446771;