chr6-30103770-C-T

Variant names:

• chr6-30103770-C-T
• rs17194265
• NM_007028.5:c.1044G>A

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_007028.5(TRIM31):​c.1044G>A​(p.Gly348Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00311 in 1,612,906 control chromosomes in the GnomAD database, including 132 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.016 (68 hom., cov: 31)
  • Exomes 𝑓: 0.0018 (64 hom.)
• Consequence: TRIM31 NM_007028.5 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.212
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP6: Variant 6-30103770-C-T is Benign according to our data. Variant chr6-30103770-C-T is described in ClinVar as Benign. ClinVar VariationId is 788532.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.212 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007028.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM31	NM_007028.5	MANE Select	c.1044G>A	p.Gly348Gly	synonymous	Exon 9 of 9	NP_008959.3
	TRIM31	NR_134870.2		n.1154G>A		non_coding_transcript_exon	Exon 9 of 10
	TRIM31	NR_134871.2		n.1087G>A		non_coding_transcript_exon	Exon 8 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM31	ENST00000376734.4	TSL:5 MANE Select	c.1044G>A	p.Gly348Gly	synonymous	Exon 9 of 9	ENSP00000365924.3	Q9BZY9-1
	TRIM31	ENST00000873800.1		c.1044G>A	p.Gly348Gly	synonymous	Exon 8 of 8	ENSP00000543859.1
	TRIM31	ENST00000960267.1		c.1044G>A	p.Gly348Gly	synonymous	Exon 9 of 9	ENSP00000630326.1

Frequencies

GnomAD3 genomes AF: 0.0159 AC: 2414 AN: 152038 Hom.: 67 Cov.: 31

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00616

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.0110

GnomAD2 exomes AF: 0.00432 AC: 1064 AN: 246558 AF XY: 0.00337

Gnomad AFR exome AF: 0.0573

Gnomad AMR exome AF: 0.00386

Gnomad ASJ exome AF: 0.000100

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000723

Gnomad OTH exome AF: 0.00115

GnomAD4 exome AF: 0.00177 AC: 2583 AN: 1460750 Hom.: 64 Cov.: 33 AF XY: 0.00161 AC XY: 1170 AN XY: 726688

African (AFR) AF: 0.0579 AC: 1940 AN: 33478

American (AMR) AF: 0.00458 AC: 205 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.0000383 AC: 1 AN: 26134

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00201 AC: 173 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52310

Middle Eastern (MID) AF: 0.00191 AC: 11 AN: 5756

European-Non Finnish (NFE) AF: 0.0000387 AC: 43 AN: 1112010

Other (OTH) AF: 0.00348 AC: 210 AN: 60384

GnomAD4 genome AF: 0.0160 AC: 2437 AN: 152156 Hom.: 68 Cov.: 31 AF XY: 0.0160 AC XY: 1190 AN XY: 74378

African (AFR) AF: 0.0556 AC: 2308 AN: 41488

American (AMR) AF: 0.00615 AC: 94 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4808

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000103 AC: 7 AN: 67998

Other (OTH) AF: 0.0109 AC: 23 AN: 2108

Alfa AF: 0.0110 Hom.: 43

Bravo AF: 0.0185

Asia WGS AF: 0.00289 AC: 10 AN: 3478

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs17194265; hg19: chr6-30071547;