ENST00000398356.6:c.28_30delCGGinsGGT

Variant names:

• chr22-23857517-CGG-GGT
• ENST00000398356.6:c.28_30delCGGinsGGT
• SLC2A11 p.Arg10Gly

Variant summary

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

The ENST00000398356.6(SLC2A11):​c.28_30delCGGinsGGT​(p.Arg10Gly) 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: 31)
• Consequence: SLC2A11 ENST00000398356.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 0 publications found

Genes affected

SLC2A11 (HGNC:14239): (solute carrier family 2 member 11) This gene belongs to a family of proteins that mediate the transport of sugars across the cell membrane. The encoded protein transports glucose and fructose. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

ENSG00000272973 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000398356.6. 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
	SLC2A11	NM_001282864.2		c.28_30delCGGinsGGT	p.Arg10Gly	missense	N/A	NP_001269793.1	A0A087X018
	SLC2A11	NM_030807.5		c.28_30delCGGinsGGT	p.Arg10Gly	missense	N/A	NP_110434.3
	SLC2A11	NM_001024938.4		c.21+526_21+528delCGGinsGGT		intron	N/A	NP_001020109.1	Q9BYW1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A11	ENST00000398356.6	TSL:1	c.28_30delCGGinsGGT	p.Arg10Gly	missense	N/A	ENSP00000381399.2	Q9BYW1-4
	SLC2A11	ENST00000345044.10	TSL:1	c.21+526_21+528delCGGinsGGT		intron	N/A	ENSP00000342542.5	Q9BYW1-1
	SLC2A11	ENST00000467660.5	TSL:1	n.143_145delCGGinsGGT		non_coding_transcript_exon	Exon 2 of 9

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.085

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: chr22-24199704;