rs421508

Positions:

• chr5-84016631-A-G
• chr5-84016631-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005711.5(EDIL3):​c.1137+43669T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,972 control chromosomes in the GnomAD database, including 30,362 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 0.62 (30362 hom., cov: 32)
• Consequence: EDIL3 NM_005711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EDIL3	NM_005711.5	c.1137+43669T>C		intron_variant		ENST00000296591.10
EDIL3	NM_001278642.1	c.1107+43669T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EDIL3	ENST00000296591.10	c.1137+43669T>C		intron_variant		1	NM_005711.5	P1
EDIL3	ENST00000380138.3	c.1107+43669T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94660 AN: 151854 Hom.: 30339 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.623 AC: 94708 AN: 151972 Hom.: 30362 Cov.: 32 AF XY: 0.629 AC XY: 46683 AN XY: 74266

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.635

Alfa AF: 0.652 Hom.: 4096

Bravo AF: 0.605

Asia WGS AF: 0.640 AC: 2222 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.56

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: rs421508; hg19: chr5-83312450;