5-84010693-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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 (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.1138-47333G>A		intron_variant	Intron 9 of 10	ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.1108-47333G>A		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.1138-47333G>A		intron_variant	Intron 9 of 10	1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.1108-47333G>A		intron_variant	Intron 8 of 9	1		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

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.199

Alfa AF: 0.202 Hom.: 850

Bravo AF: 0.192

Asia WGS AF: 0.332 AC: 1152 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	0.66
DANN	Benign	0.23

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: rs1155794; hg19: chr5-83306512;