NM_005711.5:c.68-25601A>T

Variant names:

• chr5-84279813-T-A
• rs1445754
• NM_005711.5:c.68-25601A>T

Variant summary

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

The NM_005711.5(EDIL3):​c.68-25601A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,108 control chromosomes in the GnomAD database, including 50,608 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 0.81 (50608 hom., cov: 31)
• Consequence: EDIL3 NM_005711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 3 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 = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.68-25601A>T		intron_variant	Intron 1 of 10	ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.68-25601A>T		intron_variant	Intron 1 of 9		NP_001265571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EDIL3	ENST00000296591.10	c.68-25601A>T		intron_variant	Intron 1 of 10	1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.68-25601A>T		intron_variant	Intron 1 of 9	1		ENSP00000369483.3

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123540 AN: 151990 Hom.: 50559 Cov.: 31

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.813 AC: 123645 AN: 152108 Hom.: 50608 Cov.: 31 AF XY: 0.815 AC XY: 60608 AN XY: 74332

African (AFR) AF: 0.900 AC: 37378 AN: 41518

American (AMR) AF: 0.821 AC: 12556 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2922 AN: 3472

East Asian (EAS) AF: 0.954 AC: 4918 AN: 5156

South Asian (SAS) AF: 0.773 AC: 3726 AN: 4820

European-Finnish (FIN) AF: 0.738 AC: 7791 AN: 10562

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51743 AN: 67972

Other (OTH) AF: 0.814 AC: 1720 AN: 2112

Alfa AF: 0.703 Hom.: 2018

Bravo AF: 0.824

Asia WGS AF: 0.830 AC: 2883 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.093
DANN	Benign	0.76
PhyloP100		-2.0
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: rs1445754; hg19: chr5-83575631;