Variant rs659445 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006709.5(EHMT2):c.329-11C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 1,611,146 control chromosomes in the GnomAD database, including 400,966 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.76 ( 44753 hom., cov: 32)

Exomes 𝑓: 0.69 ( 356213 hom. )

Consequence

EHMT2
NM_006709.5 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00002037

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.206

Variant links:

Genes affected

EHMT2 (HGNC:14129): (euchromatic histone lysine methyltransferase 2) This gene encodes a methyltransferase that methylates lysine residues of histone H3. Methylation of H3 at lysine 9 by this protein results in recruitment of additional epigenetic regulators and repression of transcription. This gene was initially thought to be two different genes, NG36 and G9a, adjacent to each other in the HLA locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

EHMT2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 6-31896527-G-A is Benign according to our data. Variant chr6-31896527-G-A is described in ClinVar as [Benign]. Clinvar id is 1235703.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EHMT2	NM_006709.5 linkuse as main transcript	c.329-11C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000375537.9	NP_006700.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EHMT2	ENST00000375537.9 linkuse as main transcript	c.329-11C>T		splice_polypyrimidine_tract_variant, intron_variant		1	NM_006709.5	ENSP00000364687		Q96KQ7-1

Frequencies

GnomAD3 genomes

AF:

0.760

AC:

115533

AN:

151936

Hom.:

44692

Cov.:

show subpopulations

Gnomad AFR

AF:

0.859

Gnomad AMI

AF:

0.687

Gnomad AMR

AF:

0.868

Gnomad ASJ

AF:

0.860

Gnomad EAS

AF:

0.796

Gnomad SAS

AF:

0.876

Gnomad FIN

AF:

0.665

Gnomad MID

AF:

0.902

Gnomad NFE

AF:

0.674

Gnomad OTH

AF:

0.819

GnomAD3 exomes

AF:

0.769

AC:

188576

AN:

245158

Hom.:

74062

AF XY:

0.770

AC XY:

103031

AN XY:

133764

show subpopulations

Gnomad AFR exome

AF:

0.861

Gnomad AMR exome

AF:

0.905

Gnomad ASJ exome

AF:

0.863

Gnomad EAS exome

AF:

0.812

Gnomad SAS exome

AF:

0.883

Gnomad FIN exome

AF:

0.670

Gnomad NFE exome

AF:

0.687

Gnomad OTH exome

AF:

0.769

GnomAD4 exome

AF:

0.691

AC:

1008651

AN:

1459092

Hom.:

356213

Cov.:

AF XY:

0.699

AC XY:

507124

AN XY:

725758

show subpopulations

Gnomad4 AFR exome

AF:

0.859

Gnomad4 AMR exome

AF:

0.900

Gnomad4 ASJ exome

AF:

0.858

Gnomad4 EAS exome

AF:

0.869

Gnomad4 SAS exome

AF:

0.883

Gnomad4 FIN exome

AF:

0.660

Gnomad4 NFE exome

AF:

0.652

Gnomad4 OTH exome

AF:

0.716

GnomAD4 genome

AF:

0.761

AC:

115655

AN:

152054

Hom.:

44753

Cov.:

AF XY:

0.765

AC XY:

56896

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.859

Gnomad4 AMR

AF:

0.869

Gnomad4 ASJ

AF:

0.860

Gnomad4 EAS

AF:

0.797

Gnomad4 SAS

AF:

0.877

Gnomad4 FIN

AF:

0.665

Gnomad4 NFE

AF:

0.674

Gnomad4 OTH

AF:

0.820

Alfa

AF:

0.722

Hom.:

34679

Bravo

AF:

0.780

Asia WGS

AF:

0.880

AC:

3062

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 13, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

8.4

DANN

Benign

0.59

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000020

dbscSNV1_RF

Benign

0.0

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