chr5-84279813-T-A

Position:

• chr5-84279813-T-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• 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/exons	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.68-25601A>T		intron_variant		ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.68-25601A>T		intron_variant			NP_001265571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EDIL3	ENST00000296591.10	c.68-25601A>T		intron_variant		1	NM_005711.5	ENSP00000296591	P1
EDIL3	ENST00000380138.3	c.68-25601A>T		intron_variant		1		ENSP00000369483

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

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.814

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

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: rs1445754; hg19: chr5-83575631;