rs421508

Variant names:

• chr5-84016631-A-G
• rs421508
• NM_005711.5:c.1137+43669T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.94).
• 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 rank	MANE	Protein	UniProt
EDIL3	NM_005711.5	c.1137+43669T>C		intron_variant	Intron 9 of 10	ENST00000296591.10	NP_005702.3
EDIL3	NM_001278642.1	c.1107+43669T>C		intron_variant	Intron 8 of 9		NP_001265571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EDIL3	ENST00000296591.10	c.1137+43669T>C		intron_variant	Intron 9 of 10	1	NM_005711.5	ENSP00000296591.4
EDIL3	ENST00000380138.3	c.1107+43669T>C		intron_variant	Intron 8 of 9	1		ENSP00000369483.3

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

African (AFR) AF: 0.462 AC: 19138 AN: 41414

American (AMR) AF: 0.635 AC: 9695 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2329 AN: 3472

East Asian (EAS) AF: 0.750 AC: 3874 AN: 5162

South Asian (SAS) AF: 0.589 AC: 2835 AN: 4812

European-Finnish (FIN) AF: 0.779 AC: 8237 AN: 10572

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46418 AN: 67968

Other (OTH) AF: 0.635 AC: 1339 AN: 2110

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
PhyloP100		-0.30
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: rs421508; hg19: chr5-83312450;