rs1059273

Variant names:

• chr9-98087218-G-A
• rs1059273
• NM_014788.4:c.*252C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-98087218-G-A
• chr9-98087218-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000341469.7(TRIM14):​c.*252C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000162 in 616,974 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000016 (0 hom.)
• Consequence: TRIM14 ENST00000341469.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000341469.7. 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
	TRIM14	NM_014788.4	MANE Select	c.*252C>T		3_prime_UTR	Exon 6 of 6	NP_055603.2
	TRIM14	NM_033219.3		c.*28+224C>T		intron	N/A	NP_150088.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM14	ENST00000341469.7	TSL:1 MANE Select	c.*252C>T		3_prime_UTR	Exon 6 of 6	ENSP00000344208.2
	TRIM14	ENST00000342043.3	TSL:1	c.*28+224C>T		intron	N/A	ENSP00000343990.3
	TRIM14	ENST00000375098.7	TSL:2	c.*28+224C>T		intron	N/A	ENSP00000364239.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000162 AC: 1 AN: 616974 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 336312

African (AFR) AF: 0.00 AC: 0 AN: 17464

American (AMR) AF: 0.00 AC: 0 AN: 43026

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20378

East Asian (EAS) AF: 0.0000285 AC: 1 AN: 35056

South Asian (SAS) AF: 0.00 AC: 0 AN: 68538

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51692

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4064

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 344368

Other (OTH) AF: 0.00 AC: 0 AN: 32388

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.63
DANN	Benign	0.60
PhyloP100		-0.48

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: rs1059273; hg19: chr9-100849500;