chr5-84210222-A-G

Variant names:

• chr5-84210222-A-G
• rs342410
• NM_005711.5:c.226+19633T>C

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+19633T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,990 control chromosomes in the GnomAD database, including 33,113 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 0.65 (33113 hom., cov: 33)
• Consequence: EDIL3 NM_005711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 0 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.226+19633T>C		intron_variant	Intron 3 of 10	ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.197-29701T>C		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+19633T>C		intron_variant	Intron 3 of 10	1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.197-29701T>C		intron_variant	Intron 2 of 9	1		ENSP00000369483.3

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99354 AN: 151868 Hom.: 33102 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.654 AC: 99399 AN: 151990 Hom.: 33113 Cov.: 33 AF XY: 0.654 AC XY: 48572 AN XY: 74302

African (AFR) AF: 0.540 AC: 22400 AN: 41450

American (AMR) AF: 0.592 AC: 9038 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2368 AN: 3472

East Asian (EAS) AF: 0.740 AC: 3823 AN: 5168

South Asian (SAS) AF: 0.599 AC: 2885 AN: 4820

European-Finnish (FIN) AF: 0.727 AC: 7665 AN: 10550

Middle Eastern (MID) AF: 0.655 AC: 190 AN: 290

European-Non Finnish (NFE) AF: 0.719 AC: 48870 AN: 67960

Other (OTH) AF: 0.691 AC: 1456 AN: 2108

Alfa AF: 0.667 Hom.: 30677

Bravo AF: 0.642

Asia WGS AF: 0.639 AC: 2191 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.66
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: rs342410; hg19: chr5-83506040;