Variant 2-176080455-TGCCGCGGCAGAGGCCGCGCTGTTGAGCCCCGCGGCG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM4BP6BS2

The NM_001080458.2(EVX2):c.1047_1082del(p.Gly352_Ala363del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00124 in 1,182,670 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0010 ( 0 hom., cov: 30)

Exomes 𝑓: 0.0013 ( 3 hom. )

Consequence

EVX2
NM_001080458.2 inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 6.45

Variant links:

Genes affected

EVX2 (HGNC:3507): (even-skipped homeobox 2) This gene is located at the 5' end of the HOXD gene cluster on chromosome 2. The encoded protein is a homeobox transcription factor that is related to the protein encoded by the Drosophila even-skipped (eve) gene, a member of the pair-rule class of segmentation genes. A 117 kb microdeletion at the 5' end of the HOXD gene cluster, which includes this gene and the HOXD9-HOXD13 genes, causes synpolydactyly, a dominantly inherited disease resulting in limb malformation. [provided by RefSeq, Sep 2009]

EVX2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001080458.2.

BP6

Variant 2-176080455-TGCCGCGGCAGAGGCCGCGCTGTTGAGCCCCGCGGCG-T is Benign according to our data. Variant chr2-176080455-TGCCGCGGCAGAGGCCGCGCTGTTGAGCCCCGCGGCG-T is described in ClinVar as [Likely_benign]. Clinvar id is 3046064.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAdExome4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EVX2	NM_001080458.2 linkuse as main transcript	c.1047_1082del	p.Gly352_Ala363del	inframe_deletion	3/3	ENST00000308618.5	NP_001073927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EVX2	ENST00000308618.5 linkuse as main transcript	c.1047_1082del	p.Gly352_Ala363del	inframe_deletion	3/3	5	NM_001080458.2	ENSP00000312385	P1

Frequencies

GnomAD3 genomes

AF:

0.00100

AC:

141

AN:

140962

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000155

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00173

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000610

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00162

Gnomad OTH

AF:

0.000513

GnomAD3 exomes

AF:

0.0306

AC:

AN:

980

Hom.:

AF XY:

0.0302

AC XY:

AN XY:

630

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0423

Gnomad OTH exome

AF:

0.0455

GnomAD4 exome

AF:

0.00127

AC:

1324

AN:

1041612

Hom.:

AF XY:

0.00131

AC XY:

646

AN XY:

493276

show subpopulations

Gnomad4 AFR exome

AF:

0.000141

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.0000814

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000963

Gnomad4 FIN exome

AF:

0.00149

Gnomad4 NFE exome

AF:

0.00142

Gnomad4 OTH exome

AF:

0.000568

GnomAD4 genome

AF:

0.00100

AC:

141

AN:

141058

Hom.:

Cov.:

AF XY:

0.00112

AC XY:

AN XY:

68722

show subpopulations

Gnomad4 AFR

AF:

0.000155

Gnomad4 AMR

AF:

0.00173

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000610

Gnomad4 NFE

AF:

0.00162

Gnomad4 OTH

AF:

0.000508

Alfa

AF:

0.00227

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

EVX2-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 08, 2021

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

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