1-156136137-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_170707.4(LMNA):c.1157+16G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0893 in 1,613,538 control chromosomes in the GnomAD database, including 12,322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 4497 hom., cov: 32)

Exomes 𝑓: 0.080 ( 7825 hom. )

Consequence

LMNA
NM_170707.4 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:15O:1

Conservation

PhyloP100: 0.575

Variant links:

Genes affected

LMNA (HGNC:6636): (lamin A/C) The protein encoded by this gene is part of the nuclear lamina, a two-dimensional matrix of proteins located next to the inner nuclear membrane. The lamin family of proteins make up the matrix and are highly conserved in evolution. During mitosis, the lamina matrix is reversibly disassembled as the lamin proteins are phosphorylated. Lamin proteins are thought to be involved in nuclear stability, chromatin structure and gene expression. Vertebrate lamins consist of two types, A and B. Alternative splicing results in multiple transcript variants. Mutations in this gene lead to several diseases: Emery-Dreifuss muscular dystrophy, familial partial lipodystrophy, limb girdle muscular dystrophy, dilated cardiomyopathy, Charcot-Marie-Tooth disease, and Hutchinson-Gilford progeria syndrome. [provided by RefSeq, May 2022]

LMNA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 1-156136137-G-A is Benign according to our data. Variant chr1-156136137-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 36474.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-156136137-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMNA	NM_170707.4 link	c.1157+16G>A		intron_variant	Intron 6 of 11	ENST00000368300.9	NP_733821.1	P02545-1A0A384MQX1
LMNA	NM_005572.4 link	c.1157+16G>A		intron_variant	Intron 6 of 9	ENST00000677389.1	NP_005563.1	P02545-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMNA	ENST00000368300.9 link	c.1157+16G>A		intron_variant	Intron 6 of 11	1	NM_170707.4	ENSP00000357283.4		P02545-1
LMNA	ENST00000677389.1 link	c.1157+16G>A		intron_variant	Intron 6 of 9		NM_005572.4	ENSP00000503633.1		P02545-2

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26713

AN:

152062

Hom.:

4477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.443

Gnomad AMI

AF:

0.0844

Gnomad AMR

AF:

0.0932

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.0225

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.0558

Gnomad MID

AF:

0.188

Gnomad NFE

AF:

0.0701

Gnomad OTH

AF:

0.141

GnomAD2 exomes

AF:

0.100

AC:

25124

AN:

250254

AF XY:

0.0979

show subpopulations

Gnomad AFR exome

AF:

0.459

Gnomad AMR exome

AF:

0.0650

Gnomad ASJ exome

AF:

0.130

Gnomad EAS exome

AF:

0.0191

Gnomad FIN exome

AF:

0.0551

Gnomad NFE exome

AF:

0.0713

Gnomad OTH exome

AF:

0.0890

GnomAD4 exome

AF:

0.0803

AC:

117325

AN:

1461358

Hom.:

7825

Cov.:

AF XY:

0.0820

AC XY:

59603

AN XY:

727004

show subpopulations

Gnomad4 AFR exome

AF:

0.460

AC:

15407

AN:

33472

Gnomad4 AMR exome

AF:

0.0672

AC:

3003

AN:

44718

Gnomad4 ASJ exome

AF:

0.129

AC:

3362

AN:

26132

Gnomad4 EAS exome

AF:

0.0158

AC:

626

AN:

39690

Gnomad4 SAS exome

AF:

0.135

AC:

11630

AN:

86252

Gnomad4 FIN exome

AF:

0.0535

AC:

2840

AN:

53128

Gnomad4 NFE exome

AF:

0.0661

AC:

73541

AN:

1111828

Gnomad4 Remaining exome

AF:

0.0999

AC:

6034

AN:

60388

Heterozygous variant carriers

6818

13637

20455

27274

34092

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

2936

5872

8808

11744

14680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.176

AC:

26776

AN:

152180

Hom.:

4497

Cov.:

AF XY:

0.173

AC XY:

12907

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.444

AC:

0.443852

AN:

0.443852

Gnomad4 AMR

AF:

0.0931

AC:

0.0930597

AN:

0.0930597

Gnomad4 ASJ

AF:

0.130

AC:

0.129971

AN:

0.129971

Gnomad4 EAS

AF:

0.0224

AC:

0.0224025

AN:

0.0224025

Gnomad4 SAS

AF:

0.123

AC:

0.123288

AN:

0.123288

Gnomad4 FIN

AF:

0.0558

AC:

0.0557649

AN:

0.0557649

Gnomad4 NFE

AF:

0.0701

AC:

0.0701159

AN:

0.0701159

Gnomad4 OTH

AF:

0.140

AC:

0.139546

AN:

0.139546

Heterozygous variant carriers

934

1868

2801

3735

4669

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

246

492

738

984

1230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.126

Hom.:

898

Bravo

AF:

0.189

Asia WGS

AF:

0.101

AC:

351

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:15Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:8

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 15, 2008

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Sep 19, 2013

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

not provided

Benign:3Other:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely 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

- -

Jan 27, 2021

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Epithelial Biology; Institute of Medical Biology, Singapore

Significance:not provided

Review Status:no classification provided

Collection Method:literature only

- -

Primary dilated cardiomyopathy

Benign:2

Aug 18, 2011

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Sep 27, 2022

Cohesion Phenomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Charcot-Marie-Tooth disease

Benign:1

Molecular Genetics Laboratory, London Health Sciences Centre

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Charcot-Marie-Tooth disease type 2

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

-0.84

CADD

Benign

5.2

DANN

Benign

0.39

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Mutation Taster

=100/0

polymorphism (auto)

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