Genetic Variant NM_030912.3:c.900+24delT (chr10-102655336-CT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_030912.3(TRIM8):c.900+24delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 7769 hom., cov: 0)

Exomes 𝑓: 0.28 ( 59420 hom. )

Consequence

TRIM8
NM_030912.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00200

Publications

8 publications found

Variant links:

Genes affected

TRIM8 (HGNC:15579): (tripartite motif containing 8) This gene encodes a member of the tripartite motif (TRIM) protein family. Based on similarities to other proteins, the encoded protein is suspected to be an E3 ubiquitin-protein ligase. Regulation of this gene may be altered in some cancers. Mutations resulting in a truncated protein product have been observed in early-onset epileptic encephalopathy (EOEE). [provided by RefSeq, Sep 2016]

TRIM8 Gene-Disease associations (from GenCC):

focal segmental glomerulosclerosis and neurodevelopmental syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, G2P
genetic developmental and epileptic encephalopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

TRIM8 links:

LOC105378460 (HGNC:):

LOC105378460 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM8	NM_030912.3 link	c.900+24delT		intron_variant	Intron 3 of 5	ENST00000643721.2	NP_112174.2	Q9BZR9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM8	ENST00000643721.2 link	c.900+24delT		intron_variant	Intron 3 of 5		NM_030912.3	ENSP00000496301.1		Q9BZR9

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

47299

AN:

152008

Hom.:

7768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.383

Gnomad AMI

AF:

0.0976

Gnomad AMR

AF:

0.250

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.177

Gnomad SAS

AF:

0.144

Gnomad FIN

AF:

0.329

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.296

GnomAD2 exomes

AF:

0.263

AC:

60794

AN:

230852

AF XY:

0.260

show subpopulations

Gnomad AFR exome

AF:

0.378

Gnomad AMR exome

AF:

0.184

Gnomad ASJ exome

AF:

0.293

Gnomad EAS exome

AF:

0.175

Gnomad FIN exome

AF:

0.327

Gnomad NFE exome

AF:

0.299

Gnomad OTH exome

AF:

0.281

GnomAD4 exome

AF:

0.282

AC:

406703

AN:

1443952

Hom.:

59420

Cov.:

AF XY:

0.278

AC XY:

200068

AN XY:

718790

show subpopulations

African (AFR)

AF:

0.384

AC:

12311

AN:

32096

American (AMR)

AF:

0.193

AC:

7505

AN:

38962

Ashkenazi Jewish (ASJ)

AF:

0.296

AC:

7523

AN:

25424

East Asian (EAS)

AF:

0.133

AC:

5267

AN:

39584

South Asian (SAS)

AF:

0.146

AC:

12253

AN:

83860

European-Finnish (FIN)

AF:

0.331

AC:

17653

AN:

53254

Middle Eastern (MID)

AF:

0.313

AC:

1774

AN:

5660

European-Non Finnish (NFE)

AF:

0.294

AC:

325297

AN:

1105462

Other (OTH)

AF:

0.287

AC:

17120

AN:

59650

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

14809

29617

44426

59234

74043

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10506

21012

31518

42024

52530

<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:

0.311

AC:

47304

AN:

152126

Hom.:

7769

Cov.:

AF XY:

0.307

AC XY:

22815

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.382

AC:

15851

AN:

41484

American (AMR)

AF:

0.249

AC:

3814

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.312

AC:

1083

AN:

3470

East Asian (EAS)

AF:

0.176

AC:

912

AN:

5170

South Asian (SAS)

AF:

0.143

AC:

692

AN:

4826

European-Finnish (FIN)

AF:

0.329

AC:

3477

AN:

10580

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.304

AC:

20679

AN:

67982

Other (OTH)

AF:

0.294

AC:

621

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1628

3256

4883

6511

8139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<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:

0.134

Hom.:

815

Bravo

AF:

0.309

Asia WGS

AF:

0.160

AC:

556

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.0020

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over