7-148807685-C-A

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_004456.5(EZH2):​c.2217G>T​(p.Leu739Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

EZH2
NM_004456.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.05

Publications

0 publications found
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 Gene-Disease associations (from GenCC):
  • Weaver syndrome
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P, ClinGen

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 7-148807685-C-A is Benign according to our data. Variant chr7-148807685-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 798735.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.05 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EZH2NM_004456.5 linkc.2217G>T p.Leu739Leu synonymous_variant Exon 20 of 20 ENST00000320356.7 NP_004447.2 Q15910-2A0A090N8E9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EZH2ENST00000320356.7 linkc.2217G>T p.Leu739Leu synonymous_variant Exon 20 of 20 1 NM_004456.5 ENSP00000320147.2 Q15910-2

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1444438
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
716506
African (AFR)
AF:
0.00
AC:
0
AN:
33244
American (AMR)
AF:
0.00
AC:
0
AN:
42626
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25680
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39276
South Asian (SAS)
AF:
0.00
AC:
0
AN:
82996
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
52314
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5738
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1102814
Other (OTH)
AF:
0.00
AC:
0
AN:
59750
GnomAD4 genome
Cov.:
30

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Weaver syndrome Benign:1
Jan 19, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
CADD
Benign
6.1
DANN
Benign
0.85
PhyloP100
-1.1

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

Other links and lift over

dbSNP: rs1584844275; hg19: chr7-148504777; API