17-5169019-TCC-AGT

Variant names:

• chr17-5169019-TCC-AGT
• NM_001304284.2:c.3481_3483delTCCinsAGT
• USP6 p.1162

Variant summary

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

The NM_001304284.2(USP6):​c.3481_3483delTCCinsAGT​(p.1162) variant causes a synonymous change. 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: 32)
• Consequence: USP6 NM_001304284.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.96
• Publications: 0 publications found

Genes affected

USP6 (HGNC:12629): (ubiquitin specific peptidase 6) Enables thiol-dependent deubiquitinase. Involved in protein deubiquitination and regulation of vesicle-mediated transport. Located in plasma membrane and recycling endosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304284.2. 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
	USP6	NM_001304284.2	MANE Select	c.3481_3483delTCCinsAGT	p.1162	synonymous	N/A	NP_001291213.1	P35125-1
	USP6	NM_004505.4		c.3481_3483delTCCinsAGT	p.1162	synonymous	N/A	NP_004496.2	P35125-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP6	ENST00000574788.6	TSL:1 MANE Select	c.3481_3483delTCCinsAGT	p.1162	synonymous	N/A	ENSP00000460380.1	P35125-1
	USP6	ENST00000250066.6	TSL:1	c.3481_3483delTCCinsAGT	p.1162	synonymous	N/A	ENSP00000250066.6	P35125-1
	USP6	ENST00000572949.5	TSL:2	n.*1008_*1010delTCCinsAGT		non_coding_transcript_exon	Exon 26 of 29	ENSP00000461581.1	P35125-3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.0

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: chr17-5072314;