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GeneBe

rs734005

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004456.5(EZH2):​c.2195+299C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,122 control chromosomes in the GnomAD database, including 38,442 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.70 ( 38442 hom., cov: 32)

Consequence

EZH2
NM_004456.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.99
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EZH2NM_004456.5 linkuse as main transcriptc.2195+299C>T intron_variant ENST00000320356.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EZH2ENST00000320356.7 linkuse as main transcriptc.2195+299C>T intron_variant 1 NM_004456.5 P4Q15910-2

Frequencies

GnomAD3 genomes
AF:
0.698
AC:
106112
AN:
152004
Hom.:
38393
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.903
Gnomad AMI
AF:
0.560
Gnomad AMR
AF:
0.688
Gnomad ASJ
AF:
0.587
Gnomad EAS
AF:
0.669
Gnomad SAS
AF:
0.610
Gnomad FIN
AF:
0.554
Gnomad MID
AF:
0.696
Gnomad NFE
AF:
0.615
Gnomad OTH
AF:
0.665
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.698
AC:
106223
AN:
152122
Hom.:
38442
Cov.:
32
AF XY:
0.695
AC XY:
51679
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.903
Gnomad4 AMR
AF:
0.689
Gnomad4 ASJ
AF:
0.587
Gnomad4 EAS
AF:
0.669
Gnomad4 SAS
AF:
0.610
Gnomad4 FIN
AF:
0.554
Gnomad4 NFE
AF:
0.615
Gnomad4 OTH
AF:
0.666
Alfa
AF:
0.497
Hom.:
1214
Bravo
AF:
0.719
Asia WGS
AF:
0.668
AC:
2324
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.33
DANN
Benign
0.63

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.

Other links and lift over

dbSNP: rs734005; hg19: chr7-148505864; API