Variant 10-86668546-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_007078.3(LDB3):c.-48G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 734,816 control chromosomes in the GnomAD database, including 5,320 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.099 ( 1006 hom., cov: 34)

Exomes 𝑓: 0.11 ( 4314 hom. )

Consequence

LDB3
NM_007078.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0920

Variant links:

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 links:

ENSG00000289258 (HGNC:):

ENSG00000289258 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 10-86668546-G-A is Benign according to our data. Variant chr10-86668546-G-A is described in ClinVar as [Benign]. Clinvar id is 138104.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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 rank	MANE	Protein	UniProt
LDB3	NM_007078.3 link	c.-48G>A		5_prime_UTR_variant	Exon 1 of 14	ENST00000361373.9	NP_009009.1	O75112-1
LDB3	NM_001368067.1 link	c.-48G>A		5_prime_UTR_variant	Exon 1 of 9	ENST00000263066.11	NP_001354996.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
LDB3	ENST00000361373 link	c.-48G>A	5_prime_UTR_variant	Exon 1 of 14	1	NM_007078.3	ENSP00000355296.3	O75112-1
LDB3	ENST00000263066 link	c.-48G>A	5_prime_UTR_variant	Exon 1 of 9	1	NM_001368067.1	ENSP00000263066.7	O75112-6
ENSG00000289258	ENST00000443292.2 link	c.1487-123G>A	intron_variant	Intron 11 of 17	1		ENSP00000393132.2	C9JWU6

Frequencies

GnomAD3 genomes

AF:

0.0990

AC:

15065

AN:

152156

Hom.:

1007

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0296

Gnomad AMI

AF:

0.311

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.0248

Gnomad SAS

AF:

0.0333

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.112

GnomAD4 exome

AF:

0.112

AC:

65449

AN:

582542

Hom.:

4314

Cov.:

AF XY:

0.110

AC XY:

34551

AN XY:

315488

show subpopulations

Gnomad4 AFR exome

AF:

0.0304

Gnomad4 AMR exome

AF:

0.0794

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.0280

Gnomad4 SAS exome

AF:

0.0363

Gnomad4 FIN exome

AF:

0.121

Gnomad4 NFE exome

AF:

0.140

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.0989

AC:

15058

AN:

152274

Hom.:

1006

Cov.:

AF XY:

0.0982

AC XY:

7310

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0295

Gnomad4 AMR

AF:

0.115

Gnomad4 ASJ

AF:

0.141

Gnomad4 EAS

AF:

0.0249

Gnomad4 SAS

AF:

0.0332

Gnomad4 FIN

AF:

0.120

Gnomad4 NFE

AF:

0.139

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.0382

Hom.:

Bravo

AF:

0.0959

Asia WGS

AF:

0.0340

AC:

117

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Aug 08, 2011

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.83

Splicing

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