Variant rs2074474 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001369521.2(TRIM39):c.939T>C(p.Pro313Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 1,611,674 control chromosomes in the GnomAD database, including 56,734 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 0.28 ( 6480 hom., cov: 31)

Exomes 𝑓: 0.25 ( 50254 hom. )

Consequence

TRIM39
NM_001369521.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.61

Variant links:

Genes affected

TRIM39 (HGNC:10065): (tripartite motif containing 39) 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 function of this protein has not been identified. This gene lies within the major histocompatibility complex class I region on chromosome 6. Alternate splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

TRIM39 links:

TRIM39-RPP21 (HGNC:38845): (TRIM39-RPP21 readthrough) This locus represents naturally occurring read-through transcription between the neighboring TRIM39 (tripartite motif-containing 39) and RPP21 (ribonuclease P/MRP 21kDa subunit) genes on chromosome 6. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]

TRIM39-RPP21 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP7

Synonymous conserved (PhyloP=-3.61 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM39	NM_001369521.2 linkuse as main transcript	c.939T>C	p.Pro313Pro	synonymous_variant	8/8	ENST00000396551.9	NP_001356450.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM39	ENST00000396551.9 linkuse as main transcript	c.939T>C	p.Pro313Pro	synonymous_variant	8/8	5	NM_001369521.2	ENSP00000379800.3		Q9HCM9-2
TRIM39-RPP21	ENST00000623385.3 linkuse as main transcript	c.939T>C	p.Pro313Pro	synonymous_variant	7/11	5		ENSP00000485378.1		A0A096LP39

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42870

AN:

151908

Hom.:

6470

Cov.:

show subpopulations

Gnomad AFR

AF:

0.292

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.389

Gnomad ASJ

AF:

0.384

Gnomad EAS

AF:

0.484

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.224

Gnomad OTH

AF:

0.309

GnomAD3 exomes

AF:

0.306

AC:

74939

AN:

244764

Hom.:

12773

AF XY:

0.300

AC XY:

40062

AN XY:

133466

show subpopulations

Gnomad AFR exome

AF:

0.294

Gnomad AMR exome

AF:

0.466

Gnomad ASJ exome

AF:

0.367

Gnomad EAS exome

AF:

0.455

Gnomad SAS exome

AF:

0.346

Gnomad FIN exome

AF:

0.267

Gnomad NFE exome

AF:

0.224

Gnomad OTH exome

AF:

0.307

GnomAD4 exome

AF:

0.250

AC:

364213

AN:

1459648

Hom.:

50254

Cov.:

AF XY:

0.251

AC XY:

182511

AN XY:

726084

show subpopulations

Gnomad4 AFR exome

AF:

0.294

Gnomad4 AMR exome

AF:

0.458

Gnomad4 ASJ exome

AF:

0.363

Gnomad4 EAS exome

AF:

0.526

Gnomad4 SAS exome

AF:

0.347

Gnomad4 FIN exome

AF:

0.264

Gnomad4 NFE exome

AF:

0.217

Gnomad4 OTH exome

AF:

0.276

GnomAD4 genome

AF:

0.282

AC:

42923

AN:

152026

Hom.:

6480

Cov.:

AF XY:

0.287

AC XY:

21329

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.292

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.384

Gnomad4 EAS

AF:

0.484

Gnomad4 SAS

AF:

0.394

Gnomad4 FIN

AF:

0.273

Gnomad4 NFE

AF:

0.224

Gnomad4 OTH

AF:

0.311

Alfa

AF:

0.252

Hom.:

8698

Bravo

AF:

0.293

Asia WGS

AF:

0.444

AC:

1544

AN:

3478

EpiCase

AF:

0.242

EpiControl

AF:

0.246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.9

DANN

Benign

0.60

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over