17-4944792-CG-CGG

Variant names:

• chr17-4944792-C-CG
• rs1057519428
• NM_015528.3:c.833dupG

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP6

The NM_015528.3(RNF167):​c.833dupG​(p.Pro279SerfsTer17) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: RNF167 NM_015528.3 frameshift
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.563
• Publications: 0 publications found

Genes affected

RNF167 (HGNC:24544): (ring finger protein 167) RNF167 is an E3 ubiquitin ligase that interacts with TSSC5 (SLC22A18; MIM 602631) and, together with UBCH6 (UBE2E1; MIM 602916), facilitates TSSC5 polyubiquitylation (Yamada and Gorbsky, 2006 [PubMed 16314844]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 17-4944792-C-CG is Benign according to our data. Variant chr17-4944792-C-CG is described in ClinVar as Benign. ClinVar VariationId is 375600.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015528.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF167	NM_015528.3	MANE Select	c.833dupG	p.Pro279SerfsTer17	frameshift	Exon 10 of 10	NP_056343.1
	RNF167	NM_001370303.1		c.905dupG	p.Pro303SerfsTer17	frameshift	Exon 11 of 11	NP_001357232.1
	RNF167	NM_001370304.1		c.905dupG	p.Pro303SerfsTer17	frameshift	Exon 12 of 12	NP_001357233.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF167	ENST00000262482.11	TSL:2 MANE Select	c.833dupG	p.Pro279SerfsTer17	frameshift	Exon 10 of 10	ENSP00000262482.6
	RNF167	ENST00000575111.5	TSL:1	c.833dupG	p.Pro279SerfsTer17	frameshift	Exon 9 of 9	ENSP00000460190.1
	RNF167	ENST00000571816.5	TSL:5	c.833dupG	p.Pro279SerfsTer17	frameshift	Exon 11 of 11	ENSP00000459324.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Renal carnitine transport defect Benign:1

Jan 24, 2017

Heart Center, Academic Medical Center Amsterdam

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.56

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: rs1057519428; hg19: chr17-4848087;