rs10483607

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000360392.4(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
ENST00000360392.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRIM9NM_001387360.1 linkuse as main transcriptc.1603+1446T>C intron_variant ENST00000684578.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRIM9ENST00000360392.4 linkuse as main transcriptc.*1396T>C 3_prime_UTR_variant 7/71 Q9C026-5
TRIM9ENST00000684578.1 linkuse as main transcriptc.1603+1446T>C intron_variant NM_001387360.1
TRIM9ENST00000298355.7 linkuse as main transcriptc.1603+1446T>C intron_variant 1 P1Q9C026-1
TRIM9ENST00000338969.9 linkuse as main transcriptc.1591+1446T>C intron_variant 2 Q9C026-4

Frequencies

GnomAD3 genomes
AF:
0.0733
AC:
11156
AN:
152134
Hom.:
644
Cov.:
33
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.:
30
AF XY:
0.0338
AC XY:
13006
AN XY:
384716
show subpopulations
Gnomad4 AFR exome
AF:
0.156
Gnomad4 AMR exome
AF:
0.0467
Gnomad4 ASJ exome
AF:
0.0144
Gnomad4 EAS exome
AF:
0.154
Gnomad4 SAS exome
AF:
0.0822
Gnomad4 FIN exome
AF:
0.0507
Gnomad4 NFE exome
AF:
0.0296
Gnomad4 OTH exome
AF:
0.0462
GnomAD4 genome
AF:
0.0733
AC:
11166
AN:
152252
Hom.:
643
Cov.:
33
AF XY:
0.0759
AC XY:
5654
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.150
Gnomad4 AMR
AF:
0.0529
Gnomad4 ASJ
AF:
0.0150
Gnomad4 EAS
AF:
0.153
Gnomad4 SAS
AF:
0.0845
Gnomad4 FIN
AF:
0.0706
Gnomad4 NFE
AF:
0.0292
Gnomad4 OTH
AF:
0.0644
Alfa
AF:
0.0394
Hom.:
201
Bravo
AF:
0.0754
Asia WGS
AF:
0.113
AC:
393
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
2.2
DANN
Benign
0.70

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10483607; hg19: chr14-51463322; API