chr9-136670698-A-G

Position:

• chr9-136670698-A-G

Variant summary

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

The NM_016215.5(EGFL7):​c.572-252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 769,306 control chromosomes in the GnomAD database, including 169,328 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 0.65 (32341 hom., cov: 36)
  • Exomes 𝑓: 0.66 (136987 hom.)
• Consequence: EGFL7 NM_016215.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

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]

EGFL7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EGFL7	NM_016215.5	c.572-252A>G		intron_variant		ENST00000308874.12	NP_057299.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EGFL7	ENST00000308874.12	c.572-252A>G		intron_variant		1	NM_016215.5	ENSP00000307843.7

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98742 AN: 152058 Hom.: 32328 Cov.: 36

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.594

GnomAD3 exomes AF: 0.667 AC: 162894 AN: 244366 Hom.: 54782 AF XY: 0.666 AC XY: 88593 AN XY: 132936

Gnomad AFR exome AF: 0.632

Gnomad AMR exome AF: 0.638

Gnomad ASJ exome AF: 0.597

Gnomad EAS exome AF: 0.863

Gnomad SAS exome AF: 0.730

Gnomad FIN exome AF: 0.702

Gnomad NFE exome AF: 0.631

Gnomad OTH exome AF: 0.636

GnomAD4 exome AF: 0.662 AC: 408710 AN: 617128 Hom.: 136987 Cov.: 4 AF XY: 0.663 AC XY: 222569 AN XY: 335644

Gnomad4 AFR exome AF: 0.630

Gnomad4 AMR exome AF: 0.636

Gnomad4 ASJ exome AF: 0.596

Gnomad4 EAS exome AF: 0.867

Gnomad4 SAS exome AF: 0.729

Gnomad4 FIN exome AF: 0.700

Gnomad4 NFE exome AF: 0.634

Gnomad4 OTH exome AF: 0.643

GnomAD4 genome AF: 0.649 AC: 98808 AN: 152178 Hom.: 32341 Cov.: 36 AF XY: 0.655 AC XY: 48713 AN XY: 74404

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.595

Alfa AF: 0.640 Hom.: 8826

Bravo AF: 0.637

Asia WGS AF: 0.748 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.59
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs4636297; hg19: chr9-139565150; COSMIC: COSV58247283; COSMIC: COSV58247283;