Variant rs112664025 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_024757.5(EHMT1):c.3375-11_3375-10delCT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0589 in 1,613,552 control chromosomes in the GnomAD database, including 3,276 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.052 ( 241 hom., cov: 32)

Exomes 𝑓: 0.060 ( 3035 hom. )

Consequence

EHMT1
NM_024757.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.0480

Variant links:

Genes affected

EHMT1 (HGNC:24650): (euchromatic histone lysine methyltransferase 1) The protein encoded by this gene is a histone methyltransferase that methylates the lysine-9 position of histone H3. This action marks the genomic region packaged with these methylated histones for transcriptional repression. This protein may be involved in the silencing of MYC- and E2F-responsive genes and therefore could play a role in the G0/G1 cell cycle transition. Defects in this gene are a cause of chromosome 9q subtelomeric deletion syndrome (9q-syndrome, also known as Kleefstra syndrome). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2017]

EHMT1 links:

EHMT1 (HGNC:):

EHMT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 9-137817423-ACT-A is Benign according to our data. Variant chr9-137817423-ACT-A is described in ClinVar as [Benign]. Clinvar id is 96154.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-137817423-ACT-A is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EHMT1	NM_024757.5 linkuse as main transcript	c.3375-11_3375-10delCT		intron_variant		ENST00000460843.6	NP_079033.4	Q9H9B1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EHMT1	ENST00000460843.6 linkuse as main transcript	c.3375-11_3375-10delCT		intron_variant		5	NM_024757.5	ENSP00000417980.1		Q9H9B1-1

Frequencies

GnomAD3 genomes

AF:

0.0515

AC:

7821

AN:

151730

Hom.:

236

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0480

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.0308

Gnomad ASJ

AF:

0.0283

Gnomad EAS

AF:

0.00174

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.0436

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0588

Gnomad OTH

AF:

0.0489

GnomAD3 exomes

AF:

0.0549

AC:

13758

AN:

250808

Hom.:

530

AF XY:

0.0594

AC XY:

8064

AN XY:

135654

show subpopulations

Gnomad AFR exome

AF:

0.0488

Gnomad AMR exome

AF:

0.0221

Gnomad ASJ exome

AF:

0.0338

Gnomad EAS exome

AF:

0.000707

Gnomad SAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.0469

Gnomad NFE exome

AF:

0.0606

Gnomad OTH exome

AF:

0.0498

GnomAD4 exome

AF:

0.0596

AC:

87168

AN:

1461704

Hom.:

3035

AF XY:

0.0617

AC XY:

44884

AN XY:

727178

show subpopulations

Gnomad4 AFR exome

AF:

0.0451

Gnomad4 AMR exome

AF:

0.0226

Gnomad4 ASJ exome

AF:

0.0339

Gnomad4 EAS exome

AF:

0.000327

Gnomad4 SAS exome

AF:

0.119

Gnomad4 FIN exome

AF:

0.0466

Gnomad4 NFE exome

AF:

0.0605

Gnomad4 OTH exome

AF:

0.0573

GnomAD4 genome

AF:

0.0516

AC:

7840

AN:

151848

Hom.:

241

Cov.:

AF XY:

0.0514

AC XY:

3813

AN XY:

74194

show subpopulations

Gnomad4 AFR

AF:

0.0483

Gnomad4 AMR

AF:

0.0306

Gnomad4 ASJ

AF:

0.0283

Gnomad4 EAS

AF:

0.00175

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.0436

Gnomad4 NFE

AF:

0.0588

Gnomad4 OTH

AF:

0.0512

Alfa

AF:

0.0508

Hom.:

Bravo

AF:

0.0484

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 26, 2013	- -

Kleefstra syndrome 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 09, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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