16-29847228-GA-AG

Variant names:

• chr16-29847228-GA-AG
• NM_005115.5:c.2297_2298delGAinsAG
• MVP p.Arg766Gln

Variant summary

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

The NM_005115.5(MVP):​c.2297_2298delGAinsAG​(p.Arg766Gln) 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MVP NM_005115.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.19
• Publications: 0 publications found

Genes affected

MVP (HGNC:7531): (major vault protein) This gene encodes the major component of the vault complex. Vaults are multi-subunit ribonucleoprotein structures that may be involved in nucleo-cytoplasmic transport. The encoded protein may play a role in multiple cellular processes by regulating the MAP kinase, JAK/STAT and phosphoinositide 3-kinase/Akt signaling pathways. The encoded protein also plays a role in multidrug resistance, and expression of this gene may be a prognostic marker for several types of cancer. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, May 2012]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005115.5. 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
	MVP	NM_005115.5	MANE Select	c.2297_2298delGAinsAG	p.Arg766Gln	missense	N/A	NP_005106.2
	MVP	NM_017458.3		c.2297_2298delGAinsAG	p.Arg766Gln	missense	N/A	NP_059447.2	Q14764
	MVP	NM_001293205.1		c.2099_2100delGAinsAG	p.Arg700Gln	missense	N/A	NP_001280134.1	Q14764

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MVP	ENST00000357402.10	TSL:1 MANE Select	c.2297_2298delGAinsAG	p.Arg766Gln	missense	N/A	ENSP00000349977.5	Q14764
	MVP	ENST00000395353.5	TSL:5	c.2297_2298delGAinsAG	p.Arg766Gln	missense	N/A	ENSP00000378760.1	Q14764
	MVP	ENST00000852129.1		c.2297_2298delGAinsAG	p.Arg766Gln	missense	N/A	ENSP00000522188.1

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		4.2

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: chr16-29858549;