5-84203825-T-C

Position:

• chr5-84203825-T-C

Variant summary

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

The NM_005711.5(EDIL3):​c.227-23304A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,976 control chromosomes in the GnomAD database, including 26,211 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 0.58 (26211 hom., cov: 32)
• Consequence: EDIL3 NM_005711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.227-23304A>G		intron_variant		ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.197-23304A>G		intron_variant			NP_001265571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EDIL3	ENST00000296591.10	c.227-23304A>G		intron_variant		1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.197-23304A>G		intron_variant		1		ENSP00000369483.3

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88368 AN: 151856 Hom.: 26187 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.582 AC: 88442 AN: 151976 Hom.: 26211 Cov.: 32 AF XY: 0.579 AC XY: 42953 AN XY: 74240

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.601

Alfa AF: 0.559 Hom.: 53909

Bravo AF: 0.588

Asia WGS AF: 0.599 AC: 2080 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.44

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: rs347344; hg19: chr5-83499643;