rs342409

chr5-84212340-C-Achr5-84212340-C-T

Variant summary

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

The NM_005711.5(EDIL3):c.226+17515G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,050 control chromosomes in the GnomAD database, including 39,327 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 0.72 (39327 hom., cov: 32)
• Consequence: EDIL3 NM_005711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

Genes affected

EDIL3 (HGNC:3173): (EGF like repeats and discoidin domains 3) The protein encoded by this gene is an integrin ligand. It plays an important role in mediating angiogenesis and may be important in vessel wall remodeling and development. It also influences endothelial cell behavior. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EDIL3	NM_005711.5	c.226+17515G>T		intron_variant		ENST00000296591.10
EDIL3	NM_001278642.1	c.197-31819G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EDIL3	ENST00000296591.10	c.226+17515G>T		intron_variant		1	NM_005711.5	P1
EDIL3	ENST00000380138.3	c.197-31819G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108831 AN: 151930 Hom.: 39280 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.716 AC: 108932 AN: 152050 Hom.: 39327 Cov.: 32 AF XY: 0.713 AC XY: 53042 AN XY: 74348

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.731

Alfa AF: 0.708 Hom.: 72394

Bravo AF: 0.715

Asia WGS AF: 0.661 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.55
Dann	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs342409; hg19: chr5-83508158;