rs2301092

Variant names:

• chr5-84067293-G-A
• rs2301092
• NM_005711.5:c.652-687C>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.652-687C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,054 control chromosomes in the GnomAD database, including 1,316 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 0.11 (1316 hom., cov: 32)
• Consequence: EDIL3 NM_005711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.652-687C>T		intron_variant	Intron 6 of 10	ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.622-687C>T		intron_variant	Intron 5 of 9		NP_001265571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EDIL3	ENST00000296591.10	c.652-687C>T		intron_variant	Intron 6 of 10	1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.622-687C>T		intron_variant	Intron 5 of 9	1		ENSP00000369483.3
EDIL3	ENST00000510271.1	n.201-687C>T		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16520 AN: 151936 Hom.: 1313 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.0678

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0319

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.0975

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

GnomAD4 genome AF: 0.109 AC: 16544 AN: 152054 Hom.: 1316 Cov.: 32 AF XY: 0.108 AC XY: 7993 AN XY: 74342

African (AFR) AF: 0.221 AC: 9155 AN: 41446

American (AMR) AF: 0.0771 AC: 1179 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0678 AC: 235 AN: 3468

East Asian (EAS) AF: 0.141 AC: 728 AN: 5168

South Asian (SAS) AF: 0.137 AC: 662 AN: 4824

European-Finnish (FIN) AF: 0.0319 AC: 338 AN: 10580

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0583 AC: 3965 AN: 67966

Other (OTH) AF: 0.0965 AC: 204 AN: 2114

Alfa AF: 0.0740 Hom.: 247

Bravo AF: 0.116

Asia WGS AF: 0.130 AC: 452 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.47
PhyloP100		-0.21
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: rs2301092; hg19: chr5-83363112;