Genetic Variant TRIM10:c.929-312G>A (chr6-30154798-C-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_006778.4(TRIM10):c.929-312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 643,068 control chromosomes in the GnomAD database, including 138,599 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 0.62 ( 29802 hom., cov: 31)

Exomes 𝑓: 0.66 ( 108797 hom. )

Consequence

TRIM10
NM_006778.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54

Publications

29 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006778.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM10	NM_006778.4	MANE Select	c.929-312G>A		intron	N/A	NP_006769.2	Q9UDY6-1
	TRIM10	NM_052828.3		c.929-312G>A		intron	N/A	NP_439893.2	Q9UDY6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM10	ENST00000449742.7	TSL:1 MANE Select	c.929-312G>A		intron	N/A	ENSP00000397073.2	Q9UDY6-1
	TRIM10	ENST00000376704.3	TSL:1	c.929-312G>A		intron	N/A	ENSP00000365894.3	Q9UDY6-2

Frequencies

GnomAD3 genomes

AF:

0.617

AC:

93779

AN:

151870

Hom.:

29796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.472

Gnomad AMI

AF:

0.815

Gnomad AMR

AF:

0.642

Gnomad ASJ

AF:

0.644

Gnomad EAS

AF:

0.840

Gnomad SAS

AF:

0.677

Gnomad FIN

AF:

0.728

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.660

Gnomad OTH

AF:

0.589

GnomAD4 exome

AF:

0.662

AC:

325246

AN:

491080

Hom.:

108797

AF XY:

0.664

AC XY:

177212

AN XY:

266982

show subpopulations

African (AFR)

AF:

0.473

AC:

6928

AN:

14654

American (AMR)

AF:

0.649

AC:

21260

AN:

32750

Ashkenazi Jewish (ASJ)

AF:

0.632

AC:

11636

AN:

18418

East Asian (EAS)

AF:

0.782

AC:

20787

AN:

26576

South Asian (SAS)

AF:

0.669

AC:

41047

AN:

61324

European-Finnish (FIN)

AF:

0.723

AC:

19778

AN:

27348

Middle Eastern (MID)

AF:

0.530

AC:

1704

AN:

3218

European-Non Finnish (NFE)

AF:

0.660

AC:

184606

AN:

279580

Other (OTH)

AF:

0.643

AC:

17500

AN:

27212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

5603

11206

16810

22413

28016

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

850

1700

2550

3400

4250

<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:

0.617

AC:

93828

AN:

151988

Hom.:

29802

Cov.:

AF XY:

0.622

AC XY:

46199

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.472

AC:

19554

AN:

41440

American (AMR)

AF:

0.642

AC:

9802

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.644

AC:

2234

AN:

3468

East Asian (EAS)

AF:

0.840

AC:

4321

AN:

5144

South Asian (SAS)

AF:

0.676

AC:

3255

AN:

4814

European-Finnish (FIN)

AF:

0.728

AC:

7700

AN:

10578

Middle Eastern (MID)

AF:

0.493

AC:

145

AN:

294

European-Non Finnish (NFE)

AF:

0.660

AC:

44829

AN:

67966

Other (OTH)

AF:

0.594

AC:

1248

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1759

3518

5276

7035

8794

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

774

1548

2322

3096

3870

<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:

0.626

Hom.:

36524

Bravo

AF:

0.601

Asia WGS

AF:

0.754

AC:

2621

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.24

(source)

DANN

Benign

0.51

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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