6-30147177-ACG-CGT

Variant names:

• chr6-30147177-ACG-CGT
• NM_001286633.2:c.634_636delACGinsCGT
• TRIM40 p.Thr212Arg

Variant summary

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

The NM_001286633.2(TRIM40):​c.634_636delACGinsCGT​(p.Thr212Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TRIM40 NM_001286633.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254
• Publications: 0 publications found

Genes affected

TRIM40 (HGNC:18736): (tripartite motif containing 40) This gene encodes a member of the tripartite motif (TRIM) protein family. The encoded protein may play a role as a negative regulator against inflammation and carcinogenesis in the gastrointestinal tract. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286633.2. 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
	TRIM40	NM_001286633.2	MANE Select	c.634_636delACGinsCGT	p.Thr212Arg	missense	N/A	NP_001273562.1	Q6P9F5-1
	TRIM40	NM_138700.4		c.547_549delACGinsCGT	p.Thr183Arg	missense	N/A	NP_619645.1	Q6P9F5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM40	ENST00000396581.6	TSL:1 MANE Select	c.634_636delACGinsCGT	p.Thr212Arg	missense	N/A	ENSP00000379826.1	Q6P9F5-1
	TRIM40	ENST00000307859.4	TSL:1	c.547_549delACGinsCGT	p.Thr183Arg	missense	N/A	ENSP00000308310.4	Q6P9F5-2
	TRIM40	ENST00000376724.6	TSL:2	c.634_636delACGinsCGT	p.Thr212Arg	missense	N/A	ENSP00000365914.2	Q6P9F5-1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.25

Splicing

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: chr6-30114954;