Genetic Variant KMT2D:p.Pro4170Pro (chr12-49032195-T-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_003482.4(KMT2D):c.12510A>G(p.Pro4170Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 1,612,274 control chromosomes in the GnomAD database, including 97,473 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6672 hom., cov: 33)

Exomes 𝑓: 0.35 ( 90801 hom. )

Consequence

KMT2D
NM_003482.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.643

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 12-49032195-T-C is Benign according to our data. Variant chr12-49032195-T-C is described in ClinVar as [Benign]. Clinvar id is 94158.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-49032195-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.643 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KMT2D	NM_003482.4 link	c.12510A>G	p.Pro4170Pro	synonymous_variant	Exon 40 of 55	ENST00000301067.12	NP_003473.3	O14686-1Q59FG6Q6PIA1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KMT2D	ENST00000301067.12 link	c.12510A>G	p.Pro4170Pro	synonymous_variant	Exon 40 of 55	5	NM_003482.4	ENSP00000301067.7		O14686-1

Frequencies

GnomAD3 genomes

AF:

0.267

AC:

40557

AN:

152072

Hom.:

6673

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0756

Gnomad AMI

AF:

0.331

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.425

Gnomad SAS

AF:

0.423

Gnomad FIN

AF:

0.358

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.262

GnomAD3 exomes

AF:

0.321

AC:

79586

AN:

247818

Hom.:

13888

AF XY:

0.332

AC XY:

44669

AN XY:

134580

show subpopulations

Gnomad AFR exome

AF:

0.0641

Gnomad AMR exome

AF:

0.231

Gnomad ASJ exome

AF:

0.228

Gnomad EAS exome

AF:

0.437

Gnomad SAS exome

AF:

0.400

Gnomad FIN exome

AF:

0.364

Gnomad NFE exome

AF:

0.344

Gnomad OTH exome

AF:

0.324

GnomAD4 exome

AF:

0.347

AC:

506210

AN:

1460084

Hom.:

90801

Cov.:

AF XY:

0.349

AC XY:

253160

AN XY:

726044

show subpopulations

Gnomad4 AFR exome

AF:

0.0579

Gnomad4 AMR exome

AF:

0.233

Gnomad4 ASJ exome

AF:

0.232

Gnomad4 EAS exome

AF:

0.398

Gnomad4 SAS exome

AF:

0.396

Gnomad4 FIN exome

AF:

0.365

Gnomad4 NFE exome

AF:

0.357

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.267

AC:

40560

AN:

152190

Hom.:

6672

Cov.:

AF XY:

0.270

AC XY:

20067

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.0754

Gnomad4 AMR

AF:

0.258

Gnomad4 ASJ

AF:

0.219

Gnomad4 EAS

AF:

0.425

Gnomad4 SAS

AF:

0.424

Gnomad4 FIN

AF:

0.358

Gnomad4 NFE

AF:

0.350

Gnomad4 OTH

AF:

0.262

Alfa

AF:

0.318

Hom.:

3576

Bravo

AF:

0.246

Asia WGS

AF:

0.387

AC:

1345

AN:

3478

EpiCase

AF:

0.340

EpiControl

AF:

0.334

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Oct 05, 2016

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 53% of patients studied by a panel of primary immunodeficiencies. Number of patients: 50. Only high quality variants are reported. -

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:3

May 07, 2018

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Kabuki syndrome

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Kabuki syndrome 1

Benign:1

Aug 23, 2018

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: 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

-0.60

CADD

Benign

5.8

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.

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