chr5-84126049-A-T

Variant names:

• chr5-84126049-A-T
• rs348901
• NM_005711.5:c.469+11192T>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.469+11192T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 151,846 control chromosomes in the GnomAD database, including 39,413 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 0.72 (39413 hom., cov: 31)
• Consequence: EDIL3 NM_005711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.469+11192T>A		intron_variant	Intron 5 of 10	ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.439+11192T>A		intron_variant	Intron 4 of 9		NP_001265571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EDIL3	ENST00000296591.10	c.469+11192T>A		intron_variant	Intron 5 of 10	1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.439+11192T>A		intron_variant	Intron 4 of 9	1		ENSP00000369483.3
EDIL3	ENST00000507663.1	n.387+11192T>A		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109190 AN: 151728 Hom.: 39372 Cov.: 31

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.720 AC: 109287 AN: 151846 Hom.: 39413 Cov.: 31 AF XY: 0.715 AC XY: 53026 AN XY: 74214

African (AFR) AF: 0.749 AC: 31011 AN: 41416

American (AMR) AF: 0.741 AC: 11270 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2691 AN: 3472

East Asian (EAS) AF: 0.629 AC: 3243 AN: 5154

South Asian (SAS) AF: 0.662 AC: 3184 AN: 4812

European-Finnish (FIN) AF: 0.618 AC: 6528 AN: 10556

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48927 AN: 67908

Other (OTH) AF: 0.743 AC: 1570 AN: 2112

Alfa AF: 0.718 Hom.: 4592

Bravo AF: 0.733

Asia WGS AF: 0.684 AC: 2379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.86
DANN	Benign	0.44
PhyloP100		-0.95
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: rs348901; hg19: chr5-83421867;