9-136668585-GGG-CGT

Variant names:

• chr9-136668585-GGG-CGT
• NM_016215.5:c.109_111delGGGinsCGT
• EGFL7 p.Gly37Arg

Variant summary

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

The NM_016215.5(EGFL7):​c.109_111delGGGinsCGT​(p.Gly37Arg) 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: EGFL7 NM_016215.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 0 publications found

Genes affected

EGFL7 (HGNC:20594): (EGF like domain multiple 7) This gene encodes a secreted endothelial cell protein that contains two epidermal growth factor-like domains. The encoded protein may play a role in regulating vasculogenesis. This protein may be involved in the growth and proliferation of tumor cells. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016215.5. 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
	EGFL7	NM_016215.5	MANE Select	c.109_111delGGGinsCGT	p.Gly37Arg	missense	N/A	NP_057299.1	Q9UHF1
	EGFL7	NM_201446.3		c.109_111delGGGinsCGT	p.Gly37Arg	missense	N/A	NP_958854.1	Q9UHF1
	EGFL7	NR_045110.2		n.435_437delGGGinsCGT		non_coding_transcript_exon	Exon 4 of 10

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EGFL7	ENST00000308874.12	TSL:1 MANE Select	c.109_111delGGGinsCGT	p.Gly37Arg	missense	N/A	ENSP00000307843.7	Q9UHF1
	EGFL7	ENST00000371698.3	TSL:1	c.109_111delGGGinsCGT	p.Gly37Arg	missense	N/A	ENSP00000360763.3	Q9UHF1
	EGFL7	ENST00000406555.7	TSL:1	c.109_111delGGGinsCGT	p.Gly37Arg	missense	N/A	ENSP00000385639.3	Q9UHF1

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		-0.077

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: chr9-139563037;