Genetic Variant TRIM14:c.*252C>A (chr9-98087218-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.481

Publications

17 publications found

Variant links:

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]

TRIM14 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

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

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TRIM14	ENST00000341469.7	TSL:1 MANE Select	c.*252C>A	3_prime_UTR	Exon 6 of 6	ENSP00000344208.2
TRIM14	ENST00000342043.3	TSL:1	c.*28+224C>A	intron	N/A	ENSP00000343990.3
TRIM14	ENST00000869651.1		c.*252C>A	3_prime_UTR	Exon 7 of 7	ENSP00000539710.1

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43483

AN:

151950

Hom.:

8078

Cov.:

show subpopulations

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.:

AF XY:

0.237

AC XY:

79552

AN XY:

336096

show subpopulations

African (AFR)

AF:

0.523

AC:

9122

AN:

17440

American (AMR)

AF:

0.223

AC:

9579

AN:

43006

Ashkenazi Jewish (ASJ)

AF:

0.214

AC:

4351

AN:

20346

East Asian (EAS)

AF:

0.0940

AC:

3294

AN:

35052

South Asian (SAS)

AF:

0.475

AC:

32558

AN:

68522

European-Finnish (FIN)

AF:

0.187

AC:

9674

AN:

51666

Middle Eastern (MID)

AF:

0.380

AC:

1540

AN:

4054

European-Non Finnish (NFE)

AF:

0.178

AC:

61115

AN:

344130

Other (OTH)

AF:

0.232

AC:

7521

AN:

32350

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

5279

10557

15836

21114

26393

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

658

1316

1974

2632

3290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.286

AC:

43515

AN:

152068

Hom.:

8084

Cov.:

AF XY:

0.287

AC XY:

21338

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.521

AC:

21578

AN:

41438

American (AMR)

AF:

0.223

AC:

3405

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.221

AC:

765

AN:

3468

East Asian (EAS)

AF:

0.125

AC:

645

AN:

5178

South Asian (SAS)

AF:

0.482

AC:

2324

AN:

4822

European-Finnish (FIN)

AF:

0.196

AC:

2075

AN:

10568

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.176

AC:

11953

AN:

67992

Other (OTH)

AF:

0.270

AC:

570

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1422

2844

4266

5688

7110

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

430

860

1290

1720

2150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.219

Hom.:

2659

Bravo

AF:

0.292

Asia WGS

AF:

0.333

AC:

1162

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.47

(source)

DANN

Benign

0.61

PhyloP100

-0.48

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over