Variant 6-30108126-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_007028.5(TRIM31):c.810G>A(p.Leu270Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 1,604,824 control chromosomes in the GnomAD database, including 48,960 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 0.25 ( 5077 hom., cov: 32)

Exomes 𝑓: 0.24 ( 43883 hom. )

Consequence

TRIM31
NM_007028.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.339

Variant links:

Genes affected

TRIM31 (HGNC:16289): (tripartite motif containing 31) This gene encodes a protein that functions as an E3 ubiquitin-protein ligase. This gene shows altered expression in certain tumors and may be a negative regulator of cell growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

TRIM31 links:

TRIM31 (HGNC:):

TRIM31 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM31	NM_007028.5 linkuse as main transcript	c.810G>A	p.Leu270Leu	synonymous_variant	6/9	ENST00000376734.4	NP_008959.3	Q9BZY9-1Q2L6J1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TRIM31	ENST00000376734.4 linkuse as main transcript	c.810G>A	p.Leu270Leu	synonymous_variant	6/9	5	NM_007028.5	ENSP00000365924.3	Q9BZY9-1
TRIM31	ENST00000468264.1 linkuse as main transcript	n.74G>A		non_coding_transcript_exon_variant	1/3	3
TRIM31	ENST00000485864.5 linkuse as main transcript	n.500G>A		non_coding_transcript_exon_variant	5/6	3
TRIM31-AS1	ENST00000440874.1 linkuse as main transcript	n.273+339C>T		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38484

AN:

151926

Hom.:

5070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.311

Gnomad AMR

AF:

0.303

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.252

Gnomad SAS

AF:

0.182

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.247

Gnomad OTH

AF:

0.210

GnomAD3 exomes

AF:

0.257

AC:

63229

AN:

246390

Hom.:

8812

AF XY:

0.246

AC XY:

33068

AN XY:

134302

show subpopulations

Gnomad AFR exome

AF:

0.255

Gnomad AMR exome

AF:

0.347

Gnomad ASJ exome

AF:

0.151

Gnomad EAS exome

AF:

0.284

Gnomad SAS exome

AF:

0.153

Gnomad FIN exome

AF:

0.313

Gnomad NFE exome

AF:

0.252

Gnomad OTH exome

AF:

0.233

GnomAD4 exome

AF:

0.240

AC:

348050

AN:

1452776

Hom.:

43883

Cov.:

AF XY:

0.236

AC XY:

170766

AN XY:

723140

show subpopulations

Gnomad4 AFR exome

AF:

0.246

Gnomad4 AMR exome

AF:

0.345

Gnomad4 ASJ exome

AF:

0.145

Gnomad4 EAS exome

AF:

0.225

Gnomad4 SAS exome

AF:

0.160

Gnomad4 FIN exome

AF:

0.306

Gnomad4 NFE exome

AF:

0.242

Gnomad4 OTH exome

AF:

0.223

GnomAD4 genome

AF:

0.253

AC:

38523

AN:

152048

Hom.:

5077

Cov.:

AF XY:

0.254

AC XY:

18916

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.250

Gnomad4 AMR

AF:

0.303

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.252

Gnomad4 SAS

AF:

0.183

Gnomad4 FIN

AF:

0.310

Gnomad4 NFE

AF:

0.247

Gnomad4 OTH

AF:

0.209

Alfa

AF:

0.238

Hom.:

5413

Bravo

AF:

0.253

Asia WGS

AF:

0.183

AC:

637

AN:

3478

EpiCase

AF:

0.226

EpiControl

AF:

0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

DANN

Benign

0.52

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.83

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.83

Position offset: -2

DS_AL_spliceai

0.35

Position offset: 42

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