Variant chr6-138882869-AAGGTAAATG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2

The NM_001077706.3(ECT2L):c.2028+1_2028+9del variant causes a splice donor, splice donor 5th base, coding sequence, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00575 in 1,613,714 control chromosomes in the GnomAD database, including 125 homozygotes. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.0051 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0058 ( 119 hom. )

Consequence

ECT2L
NM_001077706.3 splice_donor, splice_donor_5th_base, coding_sequence, intron

Scores

Not classified

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 7.41

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 Likely_benign. Variant got -5 ACMG points.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00513 (782/152314) while in subpopulation EAS AF= 0.0523 (271/5184). AF 95% confidence interval is 0.0472. There are 6 homozygotes in gnomad4. There are 412 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ECT2L	NM_001077706.3 linkuse as main transcript	c.2028+1_2028+9del		splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	16/22	ENST00000541398.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ECT2L	ENST00000541398.7 linkuse as main transcript	c.2028+1_2028+9del		splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	16/22	5	NM_001077706.3	P1
ECT2L	ENST00000367682.6 linkuse as main transcript	c.2028+1_2028+9del		splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	15/21	5		P1

Frequencies

GnomAD3 genomes

AF:

0.00511

AC:

778

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00236

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.0522

Gnomad SAS

AF:

0.0368

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00284

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00605

AC:

1500

AN:

247968

Hom.:

AF XY:

0.00713

AC XY:

959

AN XY:

134466

show subpopulations

Gnomad AFR exome

AF:

0.000517

Gnomad AMR exome

AF:

0.00142

Gnomad ASJ exome

AF:

0.00358

Gnomad EAS exome

AF:

0.0295

Gnomad SAS exome

AF:

0.0221

Gnomad FIN exome

AF:

0.00112

Gnomad NFE exome

AF:

0.00159

Gnomad OTH exome

AF:

0.00332

GnomAD4 exome

AF:

0.00582

AC:

8502

AN:

1461400

Hom.:

119

AF XY:

0.00682

AC XY:

4956

AN XY:

726986

show subpopulations

Gnomad4 AFR exome

AF:

0.000717

Gnomad4 AMR exome

AF:

0.00192

Gnomad4 ASJ exome

AF:

0.00520

Gnomad4 EAS exome

AF:

0.0419

Gnomad4 SAS exome

AF:

0.0339

Gnomad4 FIN exome

AF:

0.00197

Gnomad4 NFE exome

AF:

0.00277

Gnomad4 OTH exome

AF:

0.00752

GnomAD4 genome

AF:

0.00513

AC:

782

AN:

152314

Hom.:

Cov.:

AF XY:

0.00553

AC XY:

412

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.00235

Gnomad4 ASJ

AF:

0.00461

Gnomad4 EAS

AF:

0.0523

Gnomad4 SAS

AF:

0.0373

Gnomad4 FIN

AF:

0.00151

Gnomad4 NFE

AF:

0.00284

Gnomad4 OTH

AF:

0.00851

Alfa

AF:

0.00364

Hom.:

Asia WGS

AF:

0.0610

AC:

212

AN:

3478

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

Splicing

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