6-110989049-GGT-AGC

Variant names:

• chr6-110989049-GGT-AGC
• NM_032194.3:c.178_180delGGTinsAGC
• RPF2 p.Gly60Ser

Variant summary

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

The NM_032194.3(RPF2):​c.178_180delGGTinsAGC​(p.Gly60Ser) variant causes a missense 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Benign in ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: RPF2 NM_032194.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.77
• Publications: 0 publications found

Genes affected

RPF2 (HGNC:20870): (ribosome production factor 2 homolog) Enables 5S rRNA binding activity. Involved in protein localization to nucleolus; regulation of signal transduction by p53 class mediator; and ribosomal large subunit biogenesis. Located in chromosome; nucleolus; and nucleoplasm. [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_032194.3. 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
	RPF2	NM_032194.3	MANE Select	c.178_180delGGTinsAGC	p.Gly60Ser	missense	N/A	NP_115570.1	Q9H7B2
	RPF2	NM_001289111.2		c.6-2698_6-2696delGGTinsAGC		intron	N/A	NP_001276040.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPF2	ENST00000441448.7	TSL:1 MANE Select	c.178_180delGGTinsAGC	p.Gly60Ser	missense	N/A	ENSP00000402338.2	Q9H7B2
	RPF2	ENST00000607388.1	TSL:1	n.157-2698_157-2696delGGTinsAGC		intron	N/A	ENSP00000476081.1	U3KQN5
	RPF2	ENST00000885104.1		c.178_180delGGTinsAGC	p.Gly60Ser	missense	N/A	ENSP00000555163.1

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		4.8

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: chr6-111310252;