NM_005711.5:c.68-30273G>A

Variant names:

• chr5-84284485-C-T
• rs1445748
• NM_005711.5:c.68-30273G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005711.5(EDIL3):​c.68-30273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,884 control chromosomes in the GnomAD database, including 24,285 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 0.56 (24285 hom., cov: 31)
• Consequence: EDIL3 NM_005711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005711.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EDIL3	NM_005711.5	MANE Select	c.68-30273G>A		intron	N/A	NP_005702.3
	EDIL3	NM_001278642.1		c.68-30273G>A		intron	N/A	NP_001265571.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EDIL3	ENST00000296591.10	TSL:1 MANE Select	c.68-30273G>A		intron	N/A	ENSP00000296591.4
	EDIL3	ENST00000380138.3	TSL:1	c.68-30273G>A		intron	N/A	ENSP00000369483.3

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85416 AN: 151766 Hom.: 24277 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.563 AC: 85447 AN: 151884 Hom.: 24285 Cov.: 31 AF XY: 0.567 AC XY: 42096 AN XY: 74204

African (AFR) AF: 0.507 AC: 21022 AN: 41432

American (AMR) AF: 0.626 AC: 9542 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2025 AN: 3472

East Asian (EAS) AF: 0.820 AC: 4223 AN: 5148

South Asian (SAS) AF: 0.507 AC: 2440 AN: 4808

European-Finnish (FIN) AF: 0.557 AC: 5871 AN: 10544

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38508 AN: 67936

Other (OTH) AF: 0.568 AC: 1194 AN: 2102

Alfa AF: 0.565 Hom.: 22165

Bravo AF: 0.568

Asia WGS AF: 0.628 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
DANN	Benign	0.63
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1445748; hg19: chr5-83580303;