chr10-86668410-G-T

Position:

• chr10-86668410-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001368064.1(LDB3):​c.-23-259G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 522,536 control chromosomes in the GnomAD database, including 19,002 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.29 (7269 hom., cov: 34)
  • Exomes 𝑓: 0.24 (11733 hom.)
• Consequence: LDB3 NM_001368064.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0320

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP6: Variant 10-86668410-G-T is Benign according to our data. Variant chr10-86668410-G-T is described in ClinVar as [Benign]. Clinvar id is 671243.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDB3	NM_001368063.1	c.-23-259G>T		intron_variant
LDB3	NM_001368064.1	c.-23-259G>T		intron_variant
LDB3	NM_001368068.1	c.-23-259G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDB3	ENST00000688001.1	c.-23-259G>T		intron_variant				A2
LDB3	ENST00000688785.1	c.-23-259G>T		intron_variant
LDB3	ENST00000691462.1	c.-23-259G>T		intron_variant
LDB3	ENST00000687856.1	c.-23-259G>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43712 AN: 152120 Hom.: 7262 Cov.: 34

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.285

GnomAD4 exome AF: 0.237 AC: 87915 AN: 370298 Hom.: 11733 Cov.: 0 AF XY: 0.235 AC XY: 46044 AN XY: 195544

Gnomad4 AFR exome AF: 0.436

Gnomad4 AMR exome AF: 0.299

Gnomad4 ASJ exome AF: 0.229

Gnomad4 EAS exome AF: 0.448

Gnomad4 SAS exome AF: 0.248

Gnomad4 FIN exome AF: 0.226

Gnomad4 NFE exome AF: 0.197

Gnomad4 OTH exome AF: 0.245

GnomAD4 genome AF: 0.287 AC: 43751 AN: 152238 Hom.: 7269 Cov.: 34 AF XY: 0.291 AC XY: 21633 AN XY: 74424

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.282

Alfa AF: 0.0969 Hom.: 120

Bravo AF: 0.303

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	11
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11812601; hg19: chr10-88428167;