Genetic Variant EVI5:p.Gly780Gly (chr1-92513797-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001350197.2(EVI5):c.2340T>C(p.Gly780Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 1,612,986 control chromosomes in the GnomAD database, including 547,967 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.85 ( 55466 hom., cov: 26)

Exomes 𝑓: 0.82 ( 492501 hom. )

Consequence

EVI5
NM_001350197.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.00600

Variant links:

Genes affected

EVI5 (HGNC:3501): (ecotropic viral integration site 5) Enables GTPase activator activity and small GTPase binding activity. Involved in positive regulation of GTPase activity and retrograde transport, endosome to Golgi. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

EVI5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 1-92513797-A-G is Benign according to our data. Variant chr1-92513797-A-G is described in ClinVar as [Benign]. Clinvar id is 402836.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.006 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EVI5	NM_001350197.2 link	c.2340T>C	p.Gly780Gly	synonymous_variant	Exon 20 of 20	ENST00000684568.2	NP_001337126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EVI5	ENST00000684568.2 link	c.2340T>C	p.Gly780Gly	synonymous_variant	Exon 20 of 20		NM_001350197.2	ENSP00000506999.1		A0A804HIC4

Frequencies

GnomAD3 genomes

AF:

0.853

AC:

129091

AN:

151390

Hom.:

55409

Cov.:

show subpopulations

Gnomad AFR

AF:

0.929

Gnomad AMI

AF:

0.819

Gnomad AMR

AF:

0.869

Gnomad ASJ

AF:

0.888

Gnomad EAS

AF:

0.969

Gnomad SAS

AF:

0.953

Gnomad FIN

AF:

0.769

Gnomad MID

AF:

0.861

Gnomad NFE

AF:

0.799

Gnomad OTH

AF:

0.836

GnomAD3 exomes

AF:

0.854

AC:

214425

AN:

251062

Hom.:

92235

AF XY:

0.855

AC XY:

115986

AN XY:

135680

show subpopulations

Gnomad AFR exome

AF:

0.927

Gnomad AMR exome

AF:

0.912

Gnomad ASJ exome

AF:

0.881

Gnomad EAS exome

AF:

0.965

Gnomad SAS exome

AF:

0.950

Gnomad FIN exome

AF:

0.778

Gnomad NFE exome

AF:

0.795

Gnomad OTH exome

AF:

0.837

GnomAD4 exome

AF:

0.819

AC:

1196817

AN:

1461476

Hom.:

492501

Cov.:

AF XY:

0.823

AC XY:

598084

AN XY:

727060

show subpopulations

Gnomad4 AFR exome

AF:

0.932

Gnomad4 AMR exome

AF:

0.909

Gnomad4 ASJ exome

AF:

0.882

Gnomad4 EAS exome

AF:

0.974

Gnomad4 SAS exome

AF:

0.950

Gnomad4 FIN exome

AF:

0.775

Gnomad4 NFE exome

AF:

0.795

Gnomad4 OTH exome

AF:

0.840

GnomAD4 genome

AF:

0.853

AC:

129211

AN:

151510

Hom.:

55466

Cov.:

AF XY:

0.856

AC XY:

63307

AN XY:

73994

show subpopulations

Gnomad4 AFR

AF:

0.929

Gnomad4 AMR

AF:

0.869

Gnomad4 ASJ

AF:

0.888

Gnomad4 EAS

AF:

0.969

Gnomad4 SAS

AF:

0.952

Gnomad4 FIN

AF:

0.769

Gnomad4 NFE

AF:

0.799

Gnomad4 OTH

AF:

0.837

Alfa

AF:

0.812

Hom.:

62675

Bravo

AF:

0.861

Asia WGS

AF:

0.954

AC:

3319

AN:

3478

EpiCase

AF:

0.796

EpiControl

AF:

0.802

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.94

DANN

Benign

0.51

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