dbSNP rs138920492: EDIL3:p.Lys255Asn (chr5-84066493-C-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

14 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 709768.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 5 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005711.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EDIL3	NM_005711.5	MANE Select	c.765G>C	p.Lys255Asn	missense	Exon 7 of 11	NP_005702.3
	EDIL3	NM_001278642.1		c.735G>C	p.Lys245Asn	missense	Exon 6 of 10	NP_001265571.1	O43854-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
EDIL3	ENST00000296591.10	TSL:1 MANE Select	c.765G>C	p.Lys255Asn	missense	Exon 7 of 11	ENSP00000296591.4	O43854-1
EDIL3	ENST00000380138.3	TSL:1	c.735G>C	p.Lys245Asn	missense	Exon 6 of 10	ENSP00000369483.3	O43854-2
EDIL3	ENST00000866584.1		c.759G>C	p.Lys253Asn	missense	Exon 7 of 11	ENSP00000536643.1

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

GnomAD2 exomes

AF:

0.00679

AC:

1701

AN:

250412

AF XY:

0.00660

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 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

African (AFR)

AF:

0.000898

AC:

AN:

33426

American (AMR)

AF:

0.00220

AC:

AN:

44490

Ashkenazi Jewish (ASJ)

AF:

0.000383

AC:

AN:

26118

East Asian (EAS)

AF:

0.00

AC:

AN:

39592

South Asian (SAS)

AF:

0.00114

AC:

AN:

85976

European-Finnish (FIN)

AF:

0.0315

AC:

1680

AN:

53404

Middle Eastern (MID)

AF:

0.000521

AC:

AN:

5762

European-Non Finnish (NFE)

AF:

0.00567

AC:

6299

AN:

1111662

Other (OTH)

AF:

0.00568

AC:

343

AN:

60340

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

438

877

1315

1754

2192

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

220

440

660

880

1100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00594

AC:

904

AN:

152256

Hom.:

Cov.:

AF XY:

0.00712

AC XY:

530

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.000818

AC:

AN:

41554

American (AMR)

AF:

0.00464

AC:

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5180

South Asian (SAS)

AF:

0.00166

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.0320

AC:

339

AN:

10598

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00650

AC:

442

AN:

68020

Other (OTH)

AF:

0.00473

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

142

190

237

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.18

BayesDel_noAF

Uncertain

-0.020

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.63

Eigen

Benign

0.071

Eigen_PC

Benign

0.10

FATHMM_MKL

Uncertain

0.86

LIST_S2

Benign

0.85

MetaRNN

Benign

0.011

MetaSVM

Uncertain

0.79

MutationAssessor

Benign

1.5

PhyloP100

0.41

PrimateAI

Uncertain

0.67

PROVEAN

Benign

-0.97

REVEL

Uncertain

0.60

Sift

Benign

0.087

Sift4G

Benign

0.27

Polyphen

0.12

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

Mutation Taster

=92/8

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over