dbSNP rs10483607: TRIM9:c.*1396T>C (chr14-50996604-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_052978.5(TRIM9):c.*1396T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0402 in 985,358 control chromosomes in the GnomAD database, including 1,341 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 0.073 ( 643 hom., cov: 33)

Exomes 𝑓: 0.034 ( 698 hom. )

Consequence

TRIM9
NM_052978.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32

Publications

2 publications found

Variant links:

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]

TRIM9 links:

Genome browser will be placed here

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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052978.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TRIM9	NM_001387360.1	MANE Select	c.1603+1446T>C	intron	N/A	NP_001374289.1	A0A804HIL7
TRIM9	NM_052978.5		c.*1396T>C	3_prime_UTR	Exon 7 of 7	NP_443210.1	Q9C026-5
TRIM9	NM_001387377.1		c.*1396T>C	3_prime_UTR	Exon 7 of 7	NP_001374306.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TRIM9	ENST00000360392.4	TSL:1	c.*1396T>C	3_prime_UTR	Exon 7 of 7	ENSP00000353561.4	Q9C026-5
TRIM9	ENST00000684578.1	MANE Select	c.1603+1446T>C	intron	N/A	ENSP00000507131.1	A0A804HIL7
TRIM9	ENST00000298355.7	TSL:1	c.1603+1446T>C	intron	N/A	ENSP00000298355.3	Q9C026-1

Frequencies

GnomAD3 genomes

AF:

0.0733

AC:

11156

AN:

152134

Hom.:

644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0528

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.0848

Gnomad FIN

AF:

0.0706

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0292

Gnomad OTH

AF:

0.0641

GnomAD4 exome

AF:

0.0341

AC:

28409

AN:

833106

Hom.:

698

Cov.:

AF XY:

0.0338

AC XY:

13006

AN XY:

384716

show subpopulations

African (AFR)

AF:

0.156

AC:

2467

AN:

15788

American (AMR)

AF:

0.0467

AC:

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.0144

AC:

AN:

5152

East Asian (EAS)

AF:

0.154

AC:

559

AN:

3628

South Asian (SAS)

AF:

0.0822

AC:

1353

AN:

16456

European-Finnish (FIN)

AF:

0.0507

AC:

AN:

276

Middle Eastern (MID)

AF:

0.0377

AC:

AN:

1620

European-Non Finnish (NFE)

AF:

0.0296

AC:

22575

AN:

761904

Other (OTH)

AF:

0.0462

AC:

1260

AN:

27298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

1570

3140

4709

6279

7849

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1274

2548

3822

5096

6370

<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:

0.0733

AC:

11166

AN:

152252

Hom.:

643

Cov.:

AF XY:

0.0759

AC XY:

5654

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.150

AC:

6208

AN:

41512

American (AMR)

AF:

0.0529

AC:

809

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

AN:

3472

East Asian (EAS)

AF:

0.153

AC:

796

AN:

5188

South Asian (SAS)

AF:

0.0845

AC:

407

AN:

4818

European-Finnish (FIN)

AF:

0.0706

AC:

750

AN:

10618

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0292

AC:

1989

AN:

68030

Other (OTH)

AF:

0.0644

AC:

136

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

483

965

1448

1930

2413

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0442

Hom.:

342

Bravo

AF:

0.0754

Asia WGS

AF:

0.113

AC:

393

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.2

(source)

DANN

Benign

0.70

PhyloP100

-1.3

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