NM_007078.3:c.690-4A>G

Variant names:

• chr10-86691892-A-G
• rs45529531
• NM_007078.3:c.690-4A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BS1 BS2

The NM_007078.3(LDB3):​c.690-4A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00261 in 1,614,060 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0042 (3 hom., cov: 33)
  • Exomes 𝑓: 0.0024 (10 hom.)
• Consequence: LDB3 NM_007078.3 splice_region, intron
• Scores: Splicing: ADA: 0.00006169
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:4 B:16
• Conservation: PhyloP100: 0.852
• Publications: 3 publications found

Genes affected

LDB3 (HGNC:15710): (LIM domain binding 3) This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. The protein encoded by this gene interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also interacts with all three members of the myozenin family. Mutations in this gene have been associated with myofibrillar myopathy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding different isoforms have been identified; all isoforms have N-terminal PDZ domains while only longer isoforms (1, 2 and 5) have C-terminal LIM domains. [provided by RefSeq, Jan 2010]

LDB3 Gene-Disease associations (from GenCC):

• myofibrillar myopathy 4

  Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• familial isolated dilated cardiomyopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• dilated cardiomyopathy

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• familial dilated cardiomyopathy

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
• arrhythmogenic right ventricular cardiomyopathy

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ENSG00000289258 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BP6: Variant 10-86691892-A-G is Benign according to our data. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448. Variant chr10-86691892-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 36448.
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0042 (639/152304) while in subpopulation AMR AF = 0.00915 (140/15306). AF 95% confidence interval is 0.00791. There are 3 homozygotes in GnomAd4. There are 293 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 3 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LDB3	NM_007078.3	c.690-4A>G		splice_region_variant, intron_variant	Intron 5 of 13	ENST00000361373.9	NP_009009.1
LDB3	NM_001368067.1	c.549-4A>G		splice_region_variant, intron_variant	Intron 6 of 8	ENST00000263066.11	NP_001354996.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDB3	ENST00000361373.9	c.690-4A>G		splice_region_variant, intron_variant	Intron 5 of 13	1	NM_007078.3	ENSP00000355296.3
LDB3	ENST00000263066.11	c.549-4A>G		splice_region_variant, intron_variant	Intron 6 of 8	1	NM_001368067.1	ENSP00000263066.7
ENSG00000289258	ENST00000443292.2	c.2199-4A>G		splice_region_variant, intron_variant	Intron 15 of 17	1		ENSP00000393132.2

Frequencies

GnomAD3 genomes AF: 0.00421 AC: 640 AN: 152186 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.00668

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00916

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00270

Gnomad OTH AF: 0.0120

GnomAD2 exomes AF: 0.00249 AC: 627 AN: 251378 AF XY: 0.00233

Gnomad AFR exome AF: 0.00708

Gnomad AMR exome AF: 0.00535

Gnomad ASJ exome AF: 0.00298

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000277

Gnomad NFE exome AF: 0.00224

Gnomad OTH exome AF: 0.00570

GnomAD4 exome AF: 0.00245 AC: 3574 AN: 1461756 Hom.: 10 Cov.: 32 AF XY: 0.00234 AC XY: 1700 AN XY: 727178

African (AFR) AF: 0.00717 AC: 240 AN: 33478

American (AMR) AF: 0.00530 AC: 237 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00363 AC: 95 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39698

South Asian (SAS) AF: 0.0000464 AC: 4 AN: 86258

European-Finnish (FIN) AF: 0.000619 AC: 33 AN: 53318

Middle Eastern (MID) AF: 0.00503 AC: 29 AN: 5768

European-Non Finnish (NFE) AF: 0.00245 AC: 2727 AN: 1111984

Other (OTH) AF: 0.00346 AC: 209 AN: 60392

GnomAD4 genome AF: 0.00420 AC: 639 AN: 152304 Hom.: 3 Cov.: 33 AF XY: 0.00393 AC XY: 293 AN XY: 74472

African (AFR) AF: 0.00666 AC: 277 AN: 41568

American (AMR) AF: 0.00915 AC: 140 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.000377 AC: 4 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00269 AC: 183 AN: 68034

Other (OTH) AF: 0.0118 AC: 25 AN: 2114

Alfa AF: 0.00333 Hom.: 4

Bravo AF: 0.00492

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.00284

EpiControl AF: 0.00362

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:4 Benign:16

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not specified Benign:7

May 30, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

690-4A>G in intron 6 of LDB3: This variant is not expected to have clinical sign ificance because it is not located within the splice consensus sequence and has been identified in 0.7% (30/4406) of African American chromosomes from a broad p opulation by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EV S; dbSNP rs45529531). -

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 07, 2016

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

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

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

May 05, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:5

-

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jul 05, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ENSG00000289258: BS2; LDB3: BP4, BS2 -

Myofibrillar myopathy 4 Uncertain:1 Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiomyopathy Benign:2

Aug 18, 2011

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

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: curation

- -

Aug 25, 2017

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Myofibrillar Myopathy, Dominant Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dilated Cardiomyopathy, Dominant Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Left ventricular noncompaction cardiomyopathy Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiovascular phenotype Benign:1

Apr 21, 2015

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.6
DANN	Benign	0.43
PhyloP100		0.85
Mutation Taster		=92/8	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000062
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

Other links and lift over

dbSNP: rs45529531; hg19: chr10-88451649;