Variant rs2286748 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_030912.3(TRIM8):c.667-128C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 1,140,794 control chromosomes in the GnomAD database, including 54,852 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 0.30 ( 6871 hom., cov: 32)

Exomes 𝑓: 0.31 ( 47981 hom. )

Consequence

TRIM8
NM_030912.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0190

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:

LOC105378460 (HGNC:):

LOC105378460 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 (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM8	NM_030912.3 linkuse as main transcript	c.667-128C>A		intron_variant		ENST00000643721.2
LOC105378460	XR_007062272.1 linkuse as main transcript	n.85+95G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM8	ENST00000643721.2 linkuse as main transcript	c.667-128C>A		intron_variant			NM_030912.3	P1

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45525

AN:

151968

Hom.:

6869

Cov.:

show subpopulations

Gnomad AFR

AF:

0.295

Gnomad AMI

AF:

0.516

Gnomad AMR

AF:

0.280

Gnomad ASJ

AF:

0.436

Gnomad EAS

AF:

0.316

Gnomad SAS

AF:

0.382

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.319

GnomAD4 exome

AF:

0.308

AC:

304569

AN:

988708

Hom.:

47981

Cov.:

AF XY:

0.311

AC XY:

156801

AN XY:

504396

show subpopulations

Gnomad4 AFR exome

AF:

0.296

Gnomad4 AMR exome

AF:

0.226

Gnomad4 ASJ exome

AF:

0.445

Gnomad4 EAS exome

AF:

0.296

Gnomad4 SAS exome

AF:

0.377

Gnomad4 FIN exome

AF:

0.229

Gnomad4 NFE exome

AF:

0.306

Gnomad4 OTH exome

AF:

0.318

GnomAD4 genome

AF:

0.300

AC:

45559

AN:

152086

Hom.:

6871

Cov.:

AF XY:

0.299

AC XY:

22190

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.295

Gnomad4 AMR

AF:

0.279

Gnomad4 ASJ

AF:

0.436

Gnomad4 EAS

AF:

0.316

Gnomad4 SAS

AF:

0.383

Gnomad4 FIN

AF:

0.227

Gnomad4 NFE

AF:

0.300

Gnomad4 OTH

AF:

0.321

Alfa

AF:

0.282

Hom.:

736

Bravo

AF:

0.298

Asia WGS

AF:

0.345

AC:

1204

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.5

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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