rs2301086

Variant names:

• chr5-84047446-G-A
• rs2301086
• NM_005711.5:c.1137+12854C>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.1137+12854C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,916 control chromosomes in the GnomAD database, including 12,551 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 0.38 (12551 hom., cov: 32)
• Consequence: EDIL3 NM_005711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.1137+12854C>T		intron_variant	Intron 9 of 10	ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.1107+12854C>T		intron_variant	Intron 8 of 9		NP_001265571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EDIL3	ENST00000296591.10	c.1137+12854C>T		intron_variant	Intron 9 of 10	1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.1107+12854C>T		intron_variant	Intron 8 of 9	1		ENSP00000369483.3
EDIL3	ENST00000510271.1	n.*160C>T		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57642 AN: 151798 Hom.: 12511 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.380 AC: 57723 AN: 151916 Hom.: 12551 Cov.: 32 AF XY: 0.374 AC XY: 27789 AN XY: 74236

African (AFR) AF: 0.606 AC: 25111 AN: 41460

American (AMR) AF: 0.349 AC: 5330 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1049 AN: 3464

East Asian (EAS) AF: 0.245 AC: 1265 AN: 5162

South Asian (SAS) AF: 0.357 AC: 1718 AN: 4818

European-Finnish (FIN) AF: 0.210 AC: 2221 AN: 10572

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 19989 AN: 67874

Other (OTH) AF: 0.349 AC: 734 AN: 2106

Alfa AF: 0.340 Hom.: 2845

Bravo AF: 0.401

Asia WGS AF: 0.330 AC: 1148 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.65
DANN	Benign	0.18
PhyloP100		0.071
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: rs2301086; hg19: chr5-83343265; COSMIC: COSV56887209; COSMIC: COSV56887209;