rs1059273

chr9-98087218-G-T

Variant summary

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

The NM_014788.4(TRIM14):c.*252C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 768,634 control chromosomes in the GnomAD database, including 27,874 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 0.29 (8084 hom., cov: 32)
  • Exomes 𝑓: 0.23 (19790 hom.)
• Consequence: TRIM14 NM_014788.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

Genes affected

TRIM14 (HGNC:16283): (tripartite motif containing 14) 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 and its function has not been determined. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM14	NM_014788.4	c.*252C>A		3_prime_UTR_variant	6/6	ENST00000341469.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM14	ENST00000341469.7	c.*252C>A		3_prime_UTR_variant	6/6	1	NM_014788.4	P1
TRIM14	ENST00000342043.3	c.*28+224C>A		intron_variant		1		P1
TRIM14	ENST00000375098.7	c.*28+224C>A		intron_variant		2		P1
TRIM14	ENST00000478530.1	n.560+224C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43483 AN: 151950 Hom.: 8078 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.269

GnomAD4 exome AF: 0.225 AC: 138754 AN: 616566 Hom.: 19790 Cov.: 5 AF XY: 0.237 AC XY: 79552 AN XY: 336096

Gnomad4 AFR exome AF: 0.523

Gnomad4 AMR exome AF: 0.223

Gnomad4 ASJ exome AF: 0.214

Gnomad4 EAS exome AF: 0.0940

Gnomad4 SAS exome AF: 0.475

Gnomad4 FIN exome AF: 0.187

Gnomad4 NFE exome AF: 0.178

Gnomad4 OTH exome AF: 0.232

GnomAD4 genome AF: 0.286 AC: 43515 AN: 152068 Hom.: 8084 Cov.: 32 AF XY: 0.287 AC XY: 21338 AN XY: 74338

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.270

Alfa AF: 0.218 Hom.: 2367

Bravo AF: 0.292

Asia WGS AF: 0.333 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.47
Dann	Benign	0.61

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: rs1059273; hg19: chr9-100849500; COSMIC: COSV52963343; COSMIC: COSV52963343;