Variant chr7-148807624-AG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_004456.5(EZH2):c.*21delC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.75 ( 44114 hom., cov: 0)

Exomes 𝑓: 0.69 ( 339386 hom. )

Consequence

EZH2
NM_004456.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0530

Variant links:

Genes affected

EZH2 (HGNC:3527): (enhancer of zeste 2 polycomb repressive complex 2 subunit) This gene encodes a member of the Polycomb-group (PcG) family. PcG family members form multimeric protein complexes, which are involved in maintaining the transcriptional repressive state of genes over successive cell generations. This protein associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. This protein may play a role in the hematopoietic and central nervous systems. Multiple alternatively splcied transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Feb 2011]

EZH2 links:

EZH2 (HGNC:):

EZH2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 7-148807624-AG-A is Benign according to our data. Variant chr7-148807624-AG-A is described in ClinVar as [Benign]. Clinvar id is 259400.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-148807624-AG-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EZH2	NM_004456.5 linkuse as main transcript	c.*21delC		3_prime_UTR_variant	20/20	ENST00000320356.7	NP_004447.2	Q15910-2A0A090N8E9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EZH2	ENST00000320356 linkuse as main transcript	c.*21delC		3_prime_UTR_variant	20/20	1	NM_004456.5	ENSP00000320147.2		Q15910-2

Frequencies

GnomAD3 genomes

AF:

0.753

AC:

114217

AN:

151728

Hom.:

44056

Cov.:

show subpopulations

Gnomad AFR

AF:

0.936

Gnomad AMI

AF:

0.706

Gnomad AMR

AF:

0.749

Gnomad ASJ

AF:

0.678

Gnomad EAS

AF:

0.671

Gnomad SAS

AF:

0.670

Gnomad FIN

AF:

0.586

Gnomad MID

AF:

0.778

Gnomad NFE

AF:

0.685

Gnomad OTH

AF:

0.736

GnomAD3 exomes

AF:

0.685

AC:

140510

AN:

205250

Hom.:

48709

AF XY:

0.677

AC XY:

74040

AN XY:

109382

show subpopulations

Gnomad AFR exome

AF:

0.934

Gnomad AMR exome

AF:

0.721

Gnomad ASJ exome

AF:

0.678

Gnomad EAS exome

AF:

0.648

Gnomad SAS exome

AF:

0.663

Gnomad FIN exome

AF:

0.595

Gnomad NFE exome

AF:

0.670

Gnomad OTH exome

AF:

0.683

GnomAD4 exome

AF:

0.688

AC:

980410

AN:

1425804

Hom.:

339386

Cov.:

AF XY:

0.687

AC XY:

485109

AN XY:

706560

show subpopulations

Gnomad4 AFR exome

AF:

0.946

Gnomad4 AMR exome

AF:

0.724

Gnomad4 ASJ exome

AF:

0.683

Gnomad4 EAS exome

AF:

0.655

Gnomad4 SAS exome

AF:

0.676

Gnomad4 FIN exome

AF:

0.608

Gnomad4 NFE exome

AF:

0.684

Gnomad4 OTH exome

AF:

0.696

GnomAD4 genome

AF:

0.753

AC:

114337

AN:

151846

Hom.:

44114

Cov.:

AF XY:

0.749

AC XY:

55535

AN XY:

74158

show subpopulations

Gnomad4 AFR

AF:

0.936

Gnomad4 AMR

AF:

0.749

Gnomad4 ASJ

AF:

0.678

Gnomad4 EAS

AF:

0.670

Gnomad4 SAS

AF:

0.670

Gnomad4 FIN

AF:

0.586

Gnomad4 NFE

AF:

0.685

Gnomad4 OTH

AF:

0.736

Alfa

AF:

0.714

Hom.:

7112

Bravo

AF:

0.774

Asia WGS

AF:

0.694

AC:

2414

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Weaver syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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