rs2675693

chr10-86667386-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001368064.1(LDB3):c.-24+538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0988 in 152,166 control chromosomes in the GnomAD database, including 999 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.099 (999 hom., cov: 33)
• Consequence: LDB3 NM_001368064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDB3	NM_001368063.1	c.-24+538C>T		intron_variant
LDB3	NM_001368064.1	c.-24+538C>T		intron_variant
LDB3	NM_001368068.1	c.-24+538C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDB3	ENST00000688001.1	c.-24+538C>T		intron_variant				A2
LDB3	ENST00000688785.1	c.-24+538C>T		intron_variant
LDB3	ENST00000691462.1	c.-24+538C>T		intron_variant
LDB3	ENST00000687856.1	c.-24+538C>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15040 AN: 152046 Hom.: 1000 Cov.: 33

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0243

Gnomad SAS AF: 0.0334

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.112

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0988 AC: 15033 AN: 152166 Hom.: 999 Cov.: 33 AF XY: 0.0982 AC XY: 7309 AN XY: 74392

Gnomad4 AFR AF: 0.0293

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0244

Gnomad4 SAS AF: 0.0332

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.111

Alfa AF: 0.113 Hom.: 146

Bravo AF: 0.0960

Asia WGS AF: 0.0340 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.0
Dann	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2675693; hg19: chr10-88427143;