6-30112590-C-A

Variant names:

• chr6-30112590-C-A
• NM_007028.5:c.216G>T
• TRIM31 p.Arg72Arg

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_007028.5(TRIM31):​c.216G>T​(p.Arg72Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TRIM31 NM_007028.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.81
• Publications: 0 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP7: Synonymous conserved (PhyloP=-5.81 with no splicing effect.

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.216G>T	p.Arg72Arg	synonymous	Exon 2 of 9	NP_008959.3
	TRIM31	NR_134870.2		n.326G>T		non_coding_transcript_exon	Exon 2 of 10
	TRIM31	NR_134871.2		n.326G>T		non_coding_transcript_exon	Exon 2 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM31	ENST00000376734.4	TSL:5 MANE Select	c.216G>T	p.Arg72Arg	synonymous	Exon 2 of 9	ENSP00000365924.3	Q9BZY9-1
	TRIM31	ENST00000873800.1		c.216G>T	p.Arg72Arg	synonymous	Exon 1 of 8	ENSP00000543859.1
	TRIM31	ENST00000960267.1		c.216G>T	p.Arg72Arg	synonymous	Exon 2 of 9	ENSP00000630326.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-5.8
PromoterAI		0.32	Neutral

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr6-30080367;