chr5-84010693-C-T

Variant names:

• chr5-84010693-C-T
• rs1155794
• NM_005711.5:c.1138-47333G>A

Variant summary

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

The NM_005711.5(EDIL3):​c.1138-47333G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,080 control chromosomes in the GnomAD database, including 3,306 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 0.20 (3306 hom., cov: 32)
• Consequence: EDIL3 NM_005711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005711.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EDIL3	NM_005711.5	MANE Select	c.1138-47333G>A		intron	N/A	NP_005702.3
	EDIL3	NM_001278642.1		c.1108-47333G>A		intron	N/A	NP_001265571.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EDIL3	ENST00000296591.10	TSL:1 MANE Select	c.1138-47333G>A		intron	N/A	ENSP00000296591.4
	EDIL3	ENST00000380138.3	TSL:1	c.1108-47333G>A		intron	N/A	ENSP00000369483.3

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30471 AN: 151962 Hom.: 3297 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.201 AC: 30502 AN: 152080 Hom.: 3306 Cov.: 32 AF XY: 0.205 AC XY: 15261 AN XY: 74326

African (AFR) AF: 0.145 AC: 6024 AN: 41516

American (AMR) AF: 0.214 AC: 3271 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2122 AN: 5154

South Asian (SAS) AF: 0.201 AC: 971 AN: 4820

European-Finnish (FIN) AF: 0.263 AC: 2775 AN: 10560

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14061 AN: 67990

Other (OTH) AF: 0.199 AC: 420 AN: 2112

Alfa AF: 0.209 Hom.: 1496

Bravo AF: 0.192

Asia WGS AF: 0.332 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.23
PhyloP100		0.081
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: rs1155794; hg19: chr5-83306512;