NM_007028.5:c.1261G>C

Variant names:

• chr6-30103553-C-G
• rs1116221
• NM_007028.5:c.1261G>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_007028.5(TRIM31):​c.1261G>C​(p.Glu421Gln) variant causes a missense 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. 17/22 in silico tools predict 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: 31)
• Consequence: TRIM31 NM_007028.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11228806).

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.1261G>C	p.Glu421Gln	missense	Exon 9 of 9	NP_008959.3
	TRIM31	NR_134870.2		n.1371G>C		non_coding_transcript_exon	Exon 9 of 10
	TRIM31	NR_134871.2		n.1304G>C		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.1261G>C	p.Glu421Gln	missense	Exon 9 of 9	ENSP00000365924.3
	TRIM31	ENST00000873800.1		c.1261G>C	p.Glu421Gln	missense	Exon 8 of 8	ENSP00000543859.1
	TRIM31	ENST00000960267.1		c.1261G>C	p.Glu421Gln	missense	Exon 9 of 9	ENSP00000630326.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 39

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	13
DANN	Benign	0.90
DEOGEN2	Benign	0.0021	T
Eigen	Benign	-0.81
Eigen_PC	Benign	-0.96
FATHMM_MKL	Benign	0.031	N
M_CAP	Benign	0.0077	T
MetaRNN	Benign	0.11	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PhyloP100		0.30
PrimateAI	Benign	0.33	T
PROVEAN	Benign	0.0	N
REVEL	Benign	0.10
Sift	Pathogenic	0.0	D
Polyphen		0.96	P
Vest4		0.040
MutPred		0.20		Gain of loop (P = 0.024)
MVP		0.58
MPC		0.43
ClinPred		0.24	T
GERP RS		1.1
Varity_R		0.052
gMVP		0.029
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs1116221; hg19: chr6-30071330;