rs34032774

Positions:

• chr10-102655336-CT-C

Variant summary

Our verdict is Benign. Variant got -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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TRIM8	NM_030912.3	c.900+24delT		intron_variant		ENST00000643721.2	NP_112174.2
TRIM8	NM_001345950.1	c.804+24delT		intron_variant			NP_001332879.1
TRIM8	NR_144321.1	n.1023+24delT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM8	ENST00000643721.2	c.900+24delT		intron_variant			NM_030912.3	ENSP00000496301.1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47299 AN: 152008 Hom.: 7768 Cov.: 0

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

GnomAD3 exomes AF: 0.263 AC: 60794 AN: 230852 Hom.: 8654 AF XY: 0.260 AC XY: 32952 AN XY: 126528

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 SAS exome AF: 0.144

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.: 14 AF XY: 0.278 AC XY: 200068 AN XY: 718790

Gnomad4 AFR exome AF: 0.384

Gnomad4 AMR exome AF: 0.193

Gnomad4 ASJ exome AF: 0.296

Gnomad4 EAS exome AF: 0.133

Gnomad4 SAS exome AF: 0.146

Gnomad4 FIN exome AF: 0.331

Gnomad4 NFE exome AF: 0.294

Gnomad4 OTH exome AF: 0.287

GnomAD4 genome AF: 0.311 AC: 47304 AN: 152126 Hom.: 7769 Cov.: 0 AF XY: 0.307 AC XY: 22815 AN XY: 74362

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.294

Alfa AF: 0.184 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

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

Other links and lift over

dbSNP: rs34032774; hg19: chr10-104415093;