chr5-84212849-T-C

Variant names:

• chr5-84212849-T-C
• rs342421
• NM_005711.5:c.226+17006A>G

Variant summary

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

The NM_005711.5(EDIL3):​c.226+17006A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,920 control chromosomes in the GnomAD database, including 36,727 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 0.69 (36727 hom., cov: 30)
• Consequence: EDIL3 NM_005711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.226+17006A>G		intron_variant	Intron 3 of 10	ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.197-32328A>G		intron_variant	Intron 2 of 9		NP_001265571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EDIL3	ENST00000296591.10	c.226+17006A>G		intron_variant	Intron 3 of 10	1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.197-32328A>G		intron_variant	Intron 2 of 9	1		ENSP00000369483.3

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105231 AN: 151804 Hom.: 36692 Cov.: 30

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.693 AC: 105313 AN: 151920 Hom.: 36727 Cov.: 30 AF XY: 0.692 AC XY: 51408 AN XY: 74264

African (AFR) AF: 0.697 AC: 28860 AN: 41408

American (AMR) AF: 0.600 AC: 9150 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2356 AN: 3472

East Asian (EAS) AF: 0.731 AC: 3762 AN: 5144

South Asian (SAS) AF: 0.593 AC: 2857 AN: 4820

European-Finnish (FIN) AF: 0.722 AC: 7627 AN: 10558

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48301 AN: 67954

Other (OTH) AF: 0.715 AC: 1510 AN: 2112

Alfa AF: 0.695 Hom.: 58936

Bravo AF: 0.688

Asia WGS AF: 0.643 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.28
DANN	Benign	0.44
PhyloP100		-1.8
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: rs342421; hg19: chr5-83508667;