rs7671482

chr4-16895501-A-C

Variant summary

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

The NM_001290.5(LDB2):c.132+2853T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,972 control chromosomes in the GnomAD database, including 12,703 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 0.41 (12703 hom., cov: 32)
• Consequence: LDB2 NM_001290.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

Genes affected

LDB2 (HGNC:6533): (LIM domain binding 2) The protein encoded by this gene belongs to the LIM-domain binding family. Members of this family are characterized by a conserved nuclear localization sequence, an amino-terminal homodimerization domain and a carboxy-terminal LIM interaction domain. These proteins function as adapter molecules to allow assembly of transcriptional regulatory complexes. Genetic association studies suggest functions for this gene in rhegmatogenous retinal detachment and coronary artery disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDB2	NM_001290.5	c.132+2853T>G		intron_variant		ENST00000304523.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDB2	ENST00000304523.10	c.132+2853T>G		intron_variant		1	NM_001290.5	P4

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61583 AN: 151854 Hom.: 12682 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.406 AC: 61655 AN: 151972 Hom.: 12703 Cov.: 32 AF XY: 0.405 AC XY: 30053 AN XY: 74290

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.407

Alfa AF: 0.422 Hom.: 3095

Bravo AF: 0.405

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.8
Dann	Benign	0.73

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

Other links and lift over

dbSNP: rs7671482; hg19: chr4-16897124;