rs28400887

chr6-30108126-C-T

Variant summary

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

The NM_007028.5(TRIM31):c.810G>A(p.Leu270=) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

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-AS1 (HGNC:39761): (TRIM31 antisense RNA 1)

ACMG classification

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	UniProt
TRIM31	NM_007028.5	c.810G>A	p.Leu270=	synonymous_variant	6/9	ENST00000376734.4
TRIM31-AS1	NR_126470.1	n.273+339C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM31	ENST00000376734.4	c.810G>A	p.Leu270=	synonymous_variant	6/9	5	NM_007028.5	P1
TRIM31-AS1	ENST00000440874.1	n.273+339C>T		intron_variant, non_coding_transcript_variant		3
TRIM31	ENST00000468264.1	n.74G>A		non_coding_transcript_exon_variant	1/3	3
TRIM31	ENST00000485864.5	n.500G>A		non_coding_transcript_exon_variant	5/6	3

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38484 AN: 151926 Hom.: 5070 Cov.: 32

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

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.: 37 AF XY: 0.236 AC XY: 170766 AN XY: 723140

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.: 32 AF XY: 0.254 AC XY: 18916 AN XY: 74348

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	17
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

Other links and lift over

dbSNP: rs28400887; hg19: chr6-30075903; COSMIC: COSV65060295; COSMIC: COSV65060295;