Variant rs73557274 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001077706.3(ECT2L):c.1051G>A(p.Glu351Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00443 in 1,613,476 control chromosomes in the GnomAD database, including 270 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.023 ( 128 hom., cov: 31)

Exomes 𝑓: 0.0025 ( 142 hom. )

Consequence

ECT2L
NM_001077706.3 missense

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 2.74

Variant links:

Genes affected

ECT2L (HGNC:21118): (epithelial cell transforming 2 like) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of catalytic activity. [provided by Alliance of Genome Resources, Apr 2022]

ECT2L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0052517354).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ECT2L	NM_001077706.3 linkuse as main transcript	c.1051G>A	p.Glu351Lys	missense_variant	9/22	ENST00000541398.7	NP_001071174.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
ECT2L	ENST00000541398.7 linkuse as main transcript	c.1051G>A	p.Glu351Lys	missense_variant	9/22	5	NM_001077706.3	ENSP00000442307	P1
ECT2L	ENST00000367682.6 linkuse as main transcript	c.1051G>A	p.Glu351Lys	missense_variant	8/21	5		ENSP00000356655	P1
ECT2L	ENST00000495970.1 linkuse as main transcript	n.39G>A		non_coding_transcript_exon_variant	1/6	3

Frequencies

GnomAD3 genomes

AF:

0.0233

AC:

3537

AN:

152074

Hom.:

127

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0799

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0117

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000235

Gnomad OTH

AF:

0.0173

GnomAD3 exomes

AF:

0.00569

AC:

1414

AN:

248584

Hom.:

AF XY:

0.00428

AC XY:

577

AN XY:

134888

show subpopulations

Gnomad AFR exome

AF:

0.0811

Gnomad AMR exome

AF:

0.00342

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000657

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000204

Gnomad OTH exome

AF:

0.00299

GnomAD4 exome

AF:

0.00246

AC:

3594

AN:

1461282

Hom.:

142

Cov.:

AF XY:

0.00211

AC XY:

1537

AN XY:

726934

show subpopulations

Gnomad4 AFR exome

AF:

0.0838

Gnomad4 AMR exome

AF:

0.00446

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000116

Gnomad4 FIN exome

AF:

0.0000187

Gnomad4 NFE exome

AF:

0.000200

Gnomad4 OTH exome

AF:

0.00553

GnomAD4 genome

AF:

0.0233

AC:

3550

AN:

152194

Hom.:

128

Cov.:

AF XY:

0.0227

AC XY:

1687

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0800

Gnomad4 AMR

AF:

0.0117

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000235

Gnomad4 OTH

AF:

0.0171

Alfa

AF:

0.00198

Hom.:

Bravo

AF:

0.0273

ESP6500AA

AF:

0.0776

AC:

299

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.00722

AC:

873

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.000273

EpiControl

AF:

0.000297

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not specified

Other:1

not provided, no classification provided

reference population

ITMI

Sep 19, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.32

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.017

T;T;T

Eigen

Uncertain

0.28

Eigen_PC

Uncertain

0.38

FATHMM_MKL

Uncertain

0.88

LIST_S2

Benign

0.72

.;.;T

MetaRNN

Benign

0.0053

T;T;T

MetaSVM

Uncertain

-0.25

MutationAssessor

Uncertain

2.4

M;M;M

MutationTaster

Benign

0.041

P;P;P

PrimateAI

Benign

0.43

PROVEAN

Benign

-2.2

N;N;.

REVEL

Benign

0.16

Sift

Benign

0.056

T;T;.

Sift4G

Uncertain

0.023

D;D;D

Polyphen

0.19

B;B;B

Vest4

0.54

MVP

0.50

MPC

0.10

ClinPred

0.021

GERP RS

5.5

Varity_R

0.092

gMVP

0.66

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