Variant 10-102644578-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_030912.3(TRIM8):c.-40A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0567 in 1,583,694 control chromosomes in the GnomAD database, including 3,808 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.089 ( 869 hom., cov: 33)

Exomes 𝑓: 0.053 ( 2939 hom. )

Consequence

TRIM8
NM_030912.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.655

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 10-102644578-A-T is Benign according to our data. Variant chr10-102644578-A-T is described in ClinVar as [Benign]. Clinvar id is 1275111.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
TRIM8	NM_030912.3 linkuse as main transcript	c.-40A>T	5_prime_UTR_variant	1/6	ENST00000643721.2	NP_112174.2
TRIM8	NM_001345950.1 linkuse as main transcript	c.-40A>T	5_prime_UTR_variant	1/5		NP_001332879.1
TRIM8	NR_144321.1 linkuse as main transcript	n.84A>T	non_coding_transcript_exon_variant	1/6

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
TRIM8	ENST00000643721.2 linkuse as main transcript	c.-40A>T	5_prime_UTR_variant	1/6		NM_030912.3	ENSP00000496301	P1
TRIM8	ENST00000302424.12 linkuse as main transcript	c.-40A>T	5_prime_UTR_variant	1/5	1		ENSP00000302120
TRIM8	ENST00000710327.1 linkuse as main transcript	c.-40A>T	5_prime_UTR_variant	1/6			ENSP00000518207	P1

Frequencies

GnomAD3 genomes

AF:

0.0888

AC:

13472

AN:

151774

Hom.:

868

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.0968

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.0367

Gnomad FIN

AF:

0.0218

Gnomad MID

AF:

0.0962

Gnomad NFE

AF:

0.0442

Gnomad OTH

AF:

0.0808

GnomAD3 exomes

AF:

0.0686

AC:

14290

AN:

208158

Hom.:

791

AF XY:

0.0646

AC XY:

7447

AN XY:

115336

show subpopulations

Gnomad AFR exome

AF:

0.159

Gnomad AMR exome

AF:

0.0794

Gnomad ASJ exome

AF:

0.115

Gnomad EAS exome

AF:

0.214

Gnomad SAS exome

AF:

0.0353

Gnomad FIN exome

AF:

0.0199

Gnomad NFE exome

AF:

0.0448

Gnomad OTH exome

AF:

0.0675

GnomAD4 exome

AF:

0.0533

AC:

76305

AN:

1431808

Hom.:

2939

Cov.:

AF XY:

0.0524

AC XY:

37277

AN XY:

711632

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.0830

Gnomad4 ASJ exome

AF:

0.119

Gnomad4 EAS exome

AF:

0.207

Gnomad4 SAS exome

AF:

0.0370

Gnomad4 FIN exome

AF:

0.0230

Gnomad4 NFE exome

AF:

0.0438

Gnomad4 OTH exome

AF:

0.0656

GnomAD4 genome

AF:

0.0888

AC:

13489

AN:

151886

Hom.:

869

Cov.:

AF XY:

0.0888

AC XY:

6595

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.165

Gnomad4 AMR

AF:

0.0967

Gnomad4 ASJ

AF:

0.114

Gnomad4 EAS

AF:

0.206

Gnomad4 SAS

AF:

0.0368

Gnomad4 FIN

AF:

0.0218

Gnomad4 NFE

AF:

0.0442

Gnomad4 OTH

AF:

0.0799

Alfa

AF:

0.0379

Hom.:

Bravo

AF:

0.0985

Asia WGS

AF:

0.123

AC:

428

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 17, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.79

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over