Variant rs12212092 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_006778.4(TRIM10):c.194G>A(p.Arg65His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0696 in 1,614,092 control chromosomes in the GnomAD database, including 5,292 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.11 ( 1328 hom., cov: 32)

Exomes 𝑓: 0.066 ( 3964 hom. )

Consequence

TRIM10
NM_006778.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.870

Variant links:

Genes affected

TRIM10 (HGNC:10072): (tripartite motif containing 10) 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. This protein localizes to cytoplasmic bodies. Studies in mice suggest that this protein plays a role in terminal differentiation of erythroid cells. Alternate splicing of this gene generates two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

TRIM10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015873015).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM10	NM_006778.4 linkuse as main transcript	c.194G>A	p.Arg65His	missense_variant	1/7	ENST00000449742.7	NP_006769.2	Q9UDY6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM10	ENST00000449742.7 linkuse as main transcript	c.194G>A	p.Arg65His	missense_variant	1/7	1	NM_006778.4	ENSP00000397073.2		Q9UDY6-1
TRIM10	ENST00000376704.3 linkuse as main transcript	c.194G>A	p.Arg65His	missense_variant	1/8	1		ENSP00000365894.3		Q9UDY6-2

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16084

AN:

152080

Hom.:

1326

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0734

Gnomad ASJ

AF:

0.0545

Gnomad EAS

AF:

0.00365

Gnomad SAS

AF:

0.0199

Gnomad FIN

AF:

0.0551

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.0721

Gnomad OTH

AF:

0.115

GnomAD3 exomes

AF:

0.0663

AC:

16667

AN:

251484

Hom.:

883

AF XY:

0.0632

AC XY:

8589

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.218

Gnomad AMR exome

AF:

0.0547

Gnomad ASJ exome

AF:

0.0556

Gnomad EAS exome

AF:

0.00304

Gnomad SAS exome

AF:

0.0236

Gnomad FIN exome

AF:

0.0561

Gnomad NFE exome

AF:

0.0724

Gnomad OTH exome

AF:

0.0721

GnomAD4 exome

AF:

0.0658

AC:

96207

AN:

1461894

Hom.:

3964

Cov.:

AF XY:

0.0644

AC XY:

46831

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.217

Gnomad4 AMR exome

AF:

0.0588

Gnomad4 ASJ exome

AF:

0.0559

Gnomad4 EAS exome

AF:

0.00214

Gnomad4 SAS exome

AF:

0.0258

Gnomad4 FIN exome

AF:

0.0559

Gnomad4 NFE exome

AF:

0.0669

Gnomad4 OTH exome

AF:

0.0710

GnomAD4 genome

AF:

0.106

AC:

16109

AN:

152198

Hom.:

1328

Cov.:

AF XY:

0.102

AC XY:

7558

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.214

Gnomad4 AMR

AF:

0.0732

Gnomad4 ASJ

AF:

0.0545

Gnomad4 EAS

AF:

0.00366

Gnomad4 SAS

AF:

0.0199

Gnomad4 FIN

AF:

0.0551

Gnomad4 NFE

AF:

0.0721

Gnomad4 OTH

AF:

0.114

Alfa

AF:

0.0757

Hom.:

1136

Bravo

AF:

0.113

TwinsUK

AF:

0.0669

AC:

248

ALSPAC

AF:

0.0656

AC:

253

ESP6500AA

AF:

0.211

AC:

928

ESP6500EA

AF:

0.0687

AC:

591

ExAC

AF:

0.0700

AC:

8503

Asia WGS

AF:

0.0220

AC:

AN:

3478

EpiCase

AF:

0.0772

EpiControl

AF:

0.0788

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.088

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0040

T;.

Eigen

Benign

-0.70

Eigen_PC

Benign

-0.67

FATHMM_MKL

Benign

0.062

MetaRNN

Benign

0.0016

T;T

MetaSVM

Benign

-0.87

MutationAssessor

Benign

1.1

L;L

PrimateAI

Benign

0.46

PROVEAN

Benign

-2.1

N;N

REVEL

Benign

0.080

Sift

Benign

0.075

T;T

Sift4G

Benign

0.24

T;T

Polyphen

0.014

B;B

Vest4

0.033

MPC

0.13

ClinPred

0.0027

GERP RS

2.6

Varity_R

0.035

gMVP

0.21

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