Variant rs138935097 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_001077706.3(ECT2L):c.1709T>C(p.Val570Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00696 in 1,613,934 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0049 ( 6 hom., cov: 31)

Exomes 𝑓: 0.0072 ( 47 hom. )

Consequence

ECT2L
NM_001077706.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: 1.51

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004579872).

BP6

Variant 6-138881000-T-C is Benign according to our data. Variant chr6-138881000-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 133996.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ECT2L	NM_001077706.3 linkuse as main transcript	c.1709T>C	p.Val570Ala	missense_variant	15/22	ENST00000541398.7	NP_001071174.1	Q008S8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ECT2L	ENST00000541398.7 linkuse as main transcript	c.1709T>C	p.Val570Ala	missense_variant	15/22	5	NM_001077706.3	ENSP00000442307.2		Q008S8
ECT2L	ENST00000367682.6 linkuse as main transcript	c.1709T>C	p.Val570Ala	missense_variant	14/21	5		ENSP00000356655.2		Q008S8

Frequencies

GnomAD3 genomes

AF:

0.00486

AC:

738

AN:

151996

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00164

Gnomad AMI

AF:

0.0297

Gnomad AMR

AF:

0.00407

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.000661

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00813

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.00421

AC:

1050

AN:

249240

Hom.:

AF XY:

0.00427

AC XY:

577

AN XY:

135232

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.00411

Gnomad ASJ exome

AF:

0.000199

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00167

Gnomad FIN exome

AF:

0.000742

Gnomad NFE exome

AF:

0.00713

Gnomad OTH exome

AF:

0.00231

GnomAD4 exome

AF:

0.00718

AC:

10503

AN:

1461820

Hom.:

Cov.:

AF XY:

0.00705

AC XY:

5129

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.00131

Gnomad4 AMR exome

AF:

0.00458

Gnomad4 ASJ exome

AF:

0.000153

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00197

Gnomad4 FIN exome

AF:

0.000861

Gnomad4 NFE exome

AF:

0.00870

Gnomad4 OTH exome

AF:

0.00594

GnomAD4 genome

AF:

0.00485

AC:

738

AN:

152114

Hom.:

Cov.:

AF XY:

0.00420

AC XY:

312

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.00164

Gnomad4 AMR

AF:

0.00406

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00146

Gnomad4 FIN

AF:

0.000661

Gnomad4 NFE

AF:

0.00814

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.00679

Hom.:

Bravo

AF:

0.00498

TwinsUK

AF:

0.00701

AC:

ALSPAC

AF:

0.00934

AC:

ESP6500AA

AF:

0.000521

AC:

ESP6500EA

AF:

0.00713

AC:

ExAC

AF:

0.00388

AC:

469

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

ECT2L: BP4, BS2 -

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

0.14

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.34

CADD

Benign

DANN

Benign

0.89

DEOGEN2

Benign

0.0052

T;T;T

Eigen

Benign

-0.53

Eigen_PC

Benign

-0.54

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.48

.;.;T

M_CAP

Benign

0.0092

MetaRNN

Benign

0.0046

T;T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

1.0

L;L;L

PrimateAI

Benign

0.40

PROVEAN

Benign

-2.0

N;N;.

REVEL

Benign

0.16

Sift

Benign

0.19

T;T;.

Sift4G

Benign

0.17

T;T;T

Polyphen

0.043

B;B;B

Vest4

0.17

MVP

0.51

MPC

0.11

ClinPred

0.0046

GERP RS

4.4

Varity_R

0.12

gMVP

0.32

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