rs1140713

chr9-136670833-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016215.5(EGFL7):c.572-117C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 964,086 control chromosomes in the GnomAD database, including 8,051 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (1258 hom., cov: 30)
  • Exomes 𝑓: 0.12 (6793 hom.)
• Consequence: EGFL7 NM_016215.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EGFL7	NM_016215.5	c.572-117C>T		intron_variant		ENST00000308874.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EGFL7	ENST00000308874.12	c.572-117C>T		intron_variant		1	NM_016215.5	P1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18942 AN: 151766 Hom.: 1256 Cov.: 30

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.00725

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.167

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.122

GnomAD4 exome AF: 0.123 AC: 99966 AN: 812204 Hom.: 6793 Cov.: 11 AF XY: 0.126 AC XY: 52111 AN XY: 414906

Gnomad4 AFR exome AF: 0.139

Gnomad4 AMR exome AF: 0.118

Gnomad4 ASJ exome AF: 0.142

Gnomad4 EAS exome AF: 0.00399

Gnomad4 SAS exome AF: 0.163

Gnomad4 FIN exome AF: 0.121

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.126

GnomAD4 genome AF: 0.125 AC: 18979 AN: 151882 Hom.: 1258 Cov.: 30 AF XY: 0.125 AC XY: 9262 AN XY: 74212

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.00727

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.122

Alfa AF: 0.128 Hom.: 146

Bravo AF: 0.124

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.76
Dann	Benign	0.62
RBP_binding_hub_radar		0.77
RBP_regulation_power_radar		1.9

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1140713; hg19: chr9-139565285;