Variant 5-84066493-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_005711.5(EDIL3):c.765G>C(p.Lys255Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00587 in 1,613,026 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0059 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0059 ( 52 hom. )

Consequence

EDIL3
NM_005711.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.413

Variant links:

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]

EDIL3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.010772765).

BP6

Variant 5-84066493-C-G is Benign according to our data. Variant chr5-84066493-C-G is described in ClinVar as [Benign]. Clinvar id is 709768.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EDIL3	NM_005711.5 linkuse as main transcript	c.765G>C	p.Lys255Asn	missense_variant	7/11	ENST00000296591.10
EDIL3	NM_001278642.1 linkuse as main transcript	c.735G>C	p.Lys245Asn	missense_variant	6/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EDIL3	ENST00000296591.10 linkuse as main transcript	c.765G>C	p.Lys255Asn	missense_variant	7/11	1	NM_005711.5	P1	O43854-1
EDIL3	ENST00000380138.3 linkuse as main transcript	c.735G>C	p.Lys245Asn	missense_variant	6/10	1			O43854-2
EDIL3	ENST00000510271.1 linkuse as main transcript	n.314G>C		non_coding_transcript_exon_variant	2/5	2

Frequencies

GnomAD3 genomes

AF:

0.00594

AC:

903

AN:

152138

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000821

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00465

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.0320

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00648

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00679

AC:

1701

AN:

250412

Hom.:

AF XY:

0.00660

AC XY:

894

AN XY:

135368

show subpopulations

Gnomad AFR exome

AF:

0.000925

Gnomad AMR exome

AF:

0.00210

Gnomad ASJ exome

AF:

0.000298

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00131

Gnomad FIN exome

AF:

0.0339

Gnomad NFE exome

AF:

0.00710

Gnomad OTH exome

AF:

0.00558

GnomAD4 exome

AF:

0.00586

AC:

8561

AN:

1460770

Hom.:

Cov.:

AF XY:

0.00566

AC XY:

4110

AN XY:

726626

show subpopulations

Gnomad4 AFR exome

AF:

0.000898

Gnomad4 AMR exome

AF:

0.00220

Gnomad4 ASJ exome

AF:

0.000383

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00114

Gnomad4 FIN exome

AF:

0.0315

Gnomad4 NFE exome

AF:

0.00567

Gnomad4 OTH exome

AF:

0.00568

GnomAD4 genome

AF:

0.00594

AC:

904

AN:

152256

Hom.:

Cov.:

AF XY:

0.00712

AC XY:

530

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.000818

Gnomad4 AMR

AF:

0.00464

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0320

Gnomad4 NFE

AF:

0.00650

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00530

Hom.:

Bravo

AF:

0.00354

TwinsUK

AF:

0.00378

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.00628

AC:

ExAC

AF:

0.00684

AC:

830

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00475

EpiControl

AF:

0.00516

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.18

BayesDel_noAF

Uncertain

-0.020

Cadd

Benign

Dann

Uncertain

1.0

DEOGEN2

Uncertain

0.63

D;.

Eigen

Benign

0.071

Eigen_PC

Benign

0.10

FATHMM_MKL

Uncertain

0.86

LIST_S2

Benign

0.85

T;T

MetaRNN

Benign

0.011

T;T

MetaSVM

Uncertain

0.79

MutationAssessor

Benign

1.5

L;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.67

PROVEAN

Benign

-0.97

N;N

REVEL

Uncertain

0.60

Sift

Benign

0.087

T;T

Sift4G

Benign

0.27

T;T

Polyphen

0.12

B;D

Vest4

0.70

MutPred

0.62

Loss of ubiquitination at K255 (P = 0.027);.;

MVP

0.98

MPC

0.97

ClinPred

0.018

GERP RS

2.1

Varity_R

0.17

gMVP

0.64

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over