rs80132640

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2

The NM_003482.4(KMT2D):c.12028T>C(p.Ser4010Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0275 in 1,613,664 control chromosomes in the GnomAD database, including 744 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 74 hom., cov: 33)

Exomes 𝑓: 0.028 ( 670 hom. )

Consequence

KMT2D
NM_003482.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10O:1

Conservation

PhyloP100: 1.97

Variant links:

Genes affected

KMT2D (HGNC:7133): (lysine methyltransferase 2D) The protein encoded by this gene is a histone methyltransferase that methylates the Lys-4 position of histone H3. The encoded protein is part of a large protein complex called ASCOM, which has been shown to be a transcriptional regulator of the beta-globin and estrogen receptor genes. Mutations in this gene have been shown to be a cause of Kabuki syndrome. [provided by RefSeq, Oct 2010]

KMT2D links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

PP2

Missense variant where missense usually causes diseases, KMT2D

BP4

Computational evidence support a benign effect (MetaRNN=0.0025769174).

BP6

Variant 12-49032677-A-G is Benign according to our data. Variant chr12-49032677-A-G is described in ClinVar as [Benign]. Clinvar id is 94154.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-49032677-A-G is described in Lovd as [Benign]. Variant chr12-49032677-A-G is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0245 (3723/152154) while in subpopulation NFE AF= 0.0348 (2366/67972). AF 95% confidence interval is 0.0336. There are 74 homozygotes in gnomad4. There are 1831 alleles in male gnomad4 subpopulation. This position pass quality control queck.

BS2

High AC in GnomAd at 3723 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KMT2D	NM_003482.4 linkuse as main transcript	c.12028T>C	p.Ser4010Pro	missense_variant	40/55	ENST00000301067.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KMT2D	ENST00000301067.12 linkuse as main transcript	c.12028T>C	p.Ser4010Pro	missense_variant	40/55	5	NM_003482.4	A2	O14686-1

Frequencies

GnomAD3 genomes

AF:

0.0245

AC:

3723

AN:

152034

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00452

Gnomad AMI

AF:

0.0242

Gnomad AMR

AF:

0.0213

Gnomad ASJ

AF:

0.0236

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0224

Gnomad FIN

AF:

0.0542

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0348

Gnomad OTH

AF:

0.0230

GnomAD3 exomes

AF:

0.0263

AC:

6520

AN:

248348

Hom.:

102

AF XY:

0.0267

AC XY:

3601

AN XY:

134948

show subpopulations

Gnomad AFR exome

AF:

0.00396

Gnomad AMR exome

AF:

0.0171

Gnomad ASJ exome

AF:

0.0210

Gnomad EAS exome

AF:

0.000222

Gnomad SAS exome

AF:

0.0260

Gnomad FIN exome

AF:

0.0480

Gnomad NFE exome

AF:

0.0325

Gnomad OTH exome

AF:

0.0295

GnomAD4 exome

AF:

0.0279

AC:

40721

AN:

1461510

Hom.:

670

Cov.:

AF XY:

0.0278

AC XY:

20239

AN XY:

727012

show subpopulations

Gnomad4 AFR exome

AF:

0.00388

Gnomad4 AMR exome

AF:

0.0174

Gnomad4 ASJ exome

AF:

0.0221

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.0261

Gnomad4 FIN exome

AF:

0.0464

Gnomad4 NFE exome

AF:

0.0295

Gnomad4 OTH exome

AF:

0.0261

GnomAD4 genome

AF:

0.0245

AC:

3723

AN:

152154

Hom.:

Cov.:

AF XY:

0.0246

AC XY:

1831

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.00455

Gnomad4 AMR

AF:

0.0213

Gnomad4 ASJ

AF:

0.0236

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.0224

Gnomad4 FIN

AF:

0.0542

Gnomad4 NFE

AF:

0.0348

Gnomad4 OTH

AF:

0.0227

Alfa

AF:

0.0304

Hom.:

125

Bravo

AF:

0.0199

TwinsUK

AF:

0.0264

AC:

ALSPAC

AF:

0.0288

AC:

111

ESP6500AA

AF:

0.00455

AC:

ESP6500EA

AF:

0.0300

AC:

254

ExAC

AF:

0.0264

AC:

3200

Asia WGS

AF:

0.0130

AC:

AN:

3478

EpiCase

AF:

0.0324

EpiControl

AF:

0.0323

ClinVar

Significance: Benign

Submissions summary: Benign:10Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6Other:1

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Apr 07, 2016	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	Dec 31, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 08, 2013	- -
not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	May 14, 2018	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -

Kabuki syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.41

Cadd

Benign

Dann

Benign

0.56

DEOGEN2

Benign

0.055

Eigen

Benign

-0.68

Eigen_PC

Benign

-0.51

FATHMM_MKL

Benign

0.54

LIST_S2

Benign

0.58

MetaRNN

Benign

0.0026

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.0

MutationTaster

Benign

1.0

PrimateAI

Benign

0.47

PROVEAN

Benign

-1.3

REVEL

Benign

0.29

Sift

Pathogenic

0.0

Polyphen

0.0010

Vest4

0.27

MPC

0.19

ClinPred

0.048

GERP RS

2.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.29

gMVP

0.70

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