5-83943969-C-T

Position:

• chr5-83943969-C-T

Variant summary

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

The ENST00000296591.10(EDIL3):​c.1294-401G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,924 control chromosomes in the GnomAD database, including 5,332 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 0.26 (5332 hom., cov: 32)
• Consequence: EDIL3 ENST00000296591.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.1294-401G>A		intron_variant		ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.1264-401G>A		intron_variant			NP_001265571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EDIL3	ENST00000296591.10	c.1294-401G>A		intron_variant		1	NM_005711.5	ENSP00000296591	P1
EDIL3	ENST00000380138.3	c.1264-401G>A		intron_variant		1		ENSP00000369483

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39719 AN: 151806 Hom.: 5330 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.261 AC: 39722 AN: 151924 Hom.: 5332 Cov.: 32 AF XY: 0.261 AC XY: 19369 AN XY: 74206

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.277

Alfa AF: 0.278 Hom.: 9448

Bravo AF: 0.273

Asia WGS AF: 0.241 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
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: rs13153252; hg19: chr5-83239788; COSMIC: COSV56886623;